Supplementary Material (ESI) for Molecular BioSystems This journal is (c) The Royal Society of Chemistry, 2009 Assessment of helical interfaces in protein-protein interactions Andrea L. Jochimand Paramjit S. Arora Department of Chemistry New York University New York, NY 10003 Supplementary Information Page Description of methods 2 Table S1. Non-redundant Dataset of HIPP interactions 3 Table S2. Full dataset of HIPP interactions 90 Supplementary Material (ESI) for Molecular BioSystems This journal is (c) The Royal Society of Chemistry, 2009 Methods used to Identify HIPP Interactions Protein structures were obtained from the Protein Data Bank (http:://www.pdb.org/). In addition to using Rosetta, we created several computer programs to aid in our goal. The key steps to identifying HIPP interactions are listed below. 1) Using the advanced search function on the PDB website, we extract all structures with more than one protein entity. 2) Perl script to construct individual PDB files for each interacting chain within the parent PDB file. This script reads a PDB, identifies atoms from different chains that interaction with each other, then creates a new formatted PDB file with those two chains. This process is repeated until all interacting chains have a new PDB file. If the parent PDB file contains more than one structure, only the first structure is considered. 3) Perl script to identify protein partner chains between separate entities. This script reads a PDB file, identifies chains that belong to separate entities within the PDB file, and creates a list of the PDB code and partnering chains that are part of the separate entities. This enables us to find those helix interfaces that are between separate protein entities as opposed to helical interfaces between chains in a single protein. 4) Modifications within Rosetta written in C++ programming language to identify helical interfaces between interacting protein chains. Rosetta already contains programs that identify interface residues and assigns secondary structure to a protein backbone. Here we link the two routines to find protein chains with interface residues that lie within a helix. We define helical segment as one that contains at least four contiguous residues with φ and ϕ angles that are characteristic of the α-helix (φ = -47° ± 25°, ϕ = -57° ± 25°). Often, protein-protein interfaces are defined according to geometrically continuous patches of residues on the surface of a protein that exclude solvent by binding to another chain. This definition might include some residues that are not really involved in the interaction or exclude some residues that play a key role in the interaction. Therefore, we use a distance threshold between residues of different chains. 5) The length of each helix involved in HIPP interactions was calculated using a simple C++ program. 6) The PDB structures involved in HIPP interactions were classified according to molecular function. The categories were derived from those listed in the ‘Advanced Search’ option on the PDB website. 2 Supplementary Material (ESI) for Molecular BioSystems This journal is (c) The Royal Society of Chemistry, 2009 Table S1. Non-redundant Dataset of HIPP interactions PDB Code Title Classification 1A02 STRUCTURE OF THE DNA BINDING DOMAINS OF NFAT, FOS AND JUN TRANSCRIPTION/DNA BOUND TO DNA 1A2X COMPLEX OF TROPONIN C WITH A 47 RESIDUE (1-47) FRAGMENT OF COMPLEX (SKELETAL MUSCLE/MUSCLE PROTEIN) TROPONIN I 1A3R FAB FRAGMENT (ANTIBODY 8F5) COMPLEXED WITH PEPTIDE FROM VIRAL PROTEIN/IMMUNE SYSTEM HUMAN RHINOVIRUS (SEROTYPE 2) VIRAL CAPSID PROTEIN VP2 (RESIDUES 156-170) 1A4F BAR-HEADED GOOSE HEMOGLOBIN (OXY FORM) OXYGEN TRANSPORT 1A6D THERMOSOME FROM T. ACIDOPHILUM CHAPERONIN 1A6T FAB FRAGMENT OF MAB1-IA MONOCLONAL ANTIBODY TO HUMAN IMMUNOGLOBULIN RHINOVIRUS 14 NIM-IA SITE 1A81 CRYSTAL STRUCTURE OF THE TANDEM SH2 DOMAIN OF THE SYK COMPLEX (TRANSFERASE/PEPTIDE) KINASE BOUND TO A DUALLY TYROSINE-PHOSPHORYLATED ITAM 1A93 NMR SOLUTION STRUCTURE OF THE C-MYC-MAX HETERODIMERIC LEUCINE ZIPPER LEUCINE ZIPPER, NMR, MINIMIZED AVERAGE STRUCTURE 1A9N CRYSTAL STRUCTURE OF THE SPLICEOSOMAL U2B''-U2A' PROTEIN RNA BINDING PROTEIN/RNA COMPLEX BOUND TO A FRAGMENT OF U2 SMALL NUCLEAR RNA 1A9X CARBAMOYL PHOSPHATE SYNTHETASE: CAUGHT IN THE ACT OF AMIDOTRANSFERASE GLUTAMINE HYDROLYSIS 1ABR CRYSTAL STRUCTURE OF ABRIN-A COMPLEX (GLYCOSIDASE/CARBOHYDRATE) 1AD0 FAB FRAGMENT OF ENGINEERED HUMAN MONOCLONAL ANTIBODY A5B7 IMMUNOGLOBULIN 1AD9 IGG-FAB FRAGMENT OF ENGINEERED HUMAN MONOCLONAL ANTIBODY IMMUNOGLOBULIN CTM01 1AF0 SERRATIA PROTEASE IN COMPLEX WITH INHIBITOR COMPLEX (METALLOPROTEASE/INHIBITOR) 1AHG ASPARTATE AMINOTRANSFERASE HEXAMUTANT TRANSFERASE (AMINOTRANSFERASE) 1AIP EF-TU EF-TS COMPLEX FROM THERMUS THERMOPHILUS COMPLEX OF TWO ELONGATION FACTORS 1ALL ALLOPHYCOCYANIN LIGHT-HARVESTING PROTEIN 1AOI COMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B) DNA BINDING PROTEIN/DNA AND 146 BP LONG DNA FRAGMENT 1APY HUMAN ASPARTYLGLUCOSAMINIDASE HYDROLASE 1AQW GLUTATHIONE S-TRANSFERASE IN COMPLEX WITH GLUTATHIONE TRANSFERASE 1AR1 STRUCTURE AT 2.7 ANGSTROM RESOLUTION OF THE PARACOCCUS COMPLEX (OXIDOREDUCTASE/ANTIBODY) DENITRIFICANS TWO-SUBUNIT CYTOCHROME C OXIDASE COMPLEXED 3 Supplementary Material (ESI) for Molecular BioSystems This journal is (c) The Royal Society of Chemistry, 2009 WITH AN ANTIBODY FV FRAGMENT 1ARO T7 RNA POLYMERASE COMPLEXED WITH T7 LYSOZYME COMPLEX (POLYMERASE/HYDROLASE) 1ATI CRYSTAL STRUCTURE OF GLYCYL-TRNA SYNTHETASE FROM THERMUS PROTEIN BIOSYNTHESIS THERMOPHILUS 1AVO PROTEASOME ACTIVATOR REG(ALPHA) PROTEASOME ACTIVATOR 1AWC MOUSE GABP ALPHA/BETA DOMAIN BOUND TO DNA TRANSCRIPTION/DNA 1AXD STRUCTURE OF GLUTATHIONE S-TRANSFERASE-I BOUND WITH THE COMPLEX (TRANSFERASE/LIGAND) LIGAND LACTOYLGLUTATHIONE 1AXI STRUCTURAL PLASTICITY AT THE HGH:HGHBP INTERFACE COMPLEX (HORMONE/RECEPTOR) 1AY1 ANTI TAQ FAB TP7 IMMUNOGLOBULIN 1AYA CRYSTAL STRUCTURES OF PEPTIDE COMPLEXES OF THE AMINO- HYDROLASE(SH2 DOMAIN) TERMINAL SH2 DOMAIN OF THE SYP TYROSINE PHOSPHATASE 1AZS COMPLEX OF GS-ALPHA WITH THE CATALYTIC DOMAINS OF MAMMALIAN COMPLEX (LYASE/HYDROLASE) ADENYLYL CYCLASE 1B33 STRUCTURE OF LIGHT HARVESTING COMPLEX OF ALLOPHYCOCYANIN PHOTOSYNTHESIS ALPHA AND BETA CHAINS/CORE-LINKER COMPLEX AP*LC7.8 1B34 CRYSTAL STRUCTURE OF THE D1D2 SUB-COMPLEX FROM THE HUMAN RNA BINDING PROTEIN SNRNP CORE DOMAIN 1B35 CRICKET PARALYSIS VIRUS (CRPV) VIRUS 1B5F NATIVE CARDOSIN A FROM CYNARA CARDUNCULUS L. HYDROLASE 1B72 PBX1, HOMEOBOX PROTEIN HOX-B1/DNA TERNARY COMPLEX PROTEIN/DNA 1B8D CRYSTAL STRUCTURE OF A PHYCOUROBILIN-CONTAINING PHOTOSYNTHESIS PHYCOERYTHRIN 1B8H SLIDING CLAMP, DNA POLYMERASE TRANSFERASE 1B8I STRUCTURE OF THE HOMEOTIC UBX/EXD/DNA TERNARY COMPLEX TRANSCRIPTION/DNA 1BAI STRUCTURAL BASIS FOR SPECIFICITY OF RETROVIRAL PROTEASES COMPLEX (PROTEASE/INHIBITOR) 1BB1 CRYSTAL STRUCTURE OF A DESIGNED, THERMOSTABLE DE NOVO PROTEIN DESIGN HETEROTRIMERIC COILED COIL 1BBJ CRYSTAL STRUCTURE OF A CHIMERIC FAB' FRAGMENT OF AN IMMUNOGLOBULIN ANTIBODY BINDING TUMOUR CELLS 1BC5 CHEMOTAXIS RECEPTOR RECOGNITION BY PROTEIN COMPLEX (METHYLTRANSFERASE/PEPTIDE) METHYLTRANSFERASE CHER 1BFO CAMPATH-1G IGG2B RAT MONOCLONAL FAB ANTIBODY 4 Supplementary Material (ESI) for Molecular BioSystems This journal is (c) The Royal Society of Chemistry, 2009 1BH9 HTAFII18/HTAFII28 HETERODIMER CRYSTAL STRUCTURE WITH BOUND TRANSCRIPTION REGULATION COMPLEX PCMBS 1BLX P19INK4D/CDK6 COMPLEX COMPLEX (INHIBITOR PROTEIN/KINASE) 1BOG ANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH AN COMPLEX (ANTIBODY/PEPTIDE) EPITOPE-HOMOLOGOUS PEPTIDE 1BOM THREE-DIMENSIONAL STRUCTURE OF BOMBYXIN-II, AN INSULIN- INSULIN-LIKE BRAIN-SECRETORY PEPTIDE RELATED BRAIN-SECRETORY PEPTIDE OF THE SILKMOTH BOMBYX MORI: COMPARISON WITH INSULIN AND RELAXIN 1BOU THREE-DIMENSIONAL STRUCTURE OF LIGAB DIOXYGENASE 1BR1 SMOOTH MUSCLE MYOSIN MOTOR DOMAIN-ESSENTIAL LIGHT CHAIN MUSCLE PROTEIN COMPLEX WITH MGADP.ALF4 BOUND AT THE ACTIVE SITE 1BRL THREE-DIMENSIONAL STRUCTURE OF BACTERIAL LUCIFERASE FROM LUMINESCENCE VIBRIO HARVEYI AT 2.4 ANGSTROMS RESOLUTION 1BS6 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM IN COMPLEX WITH HYDROLASE TRIPEPTIDE MET-ALA-SER 1BSX STRUCTURE AND SPECIFICITY OF NUCLEAR RECEPTOR-COACTIVATOR HORMONE/GROWTH FACTOR INTERACTIONS 1BT6 P11 (S100A10), LIGAND OF ANNEXIN II IN COMPLEX WITH ANNEXIN COMPLEX (LIGAND/ANNEXIN) II N-TERMINUS 1BUN STRUCTURE OF BETA2-BUNGAROTOXIN: POTASSIUM CHANNEL BINDING TOXIN BY KUNITZ MODULES AND TARGETED PHOSPHOLIPASE ACTION 1BVY COMPLEX OF THE HEME AND FMN-BINDING DOMAINS OF THE OXIDOREDUCTASE CYTOCHROME P450(BM-3) 1BWV ACTIVATED RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LYASE (RUBISCO) COMPLEXED WITH THE REACTION INTERMEDIATE ANALOGUE 2-CARBOXYARABINITOL 1,5-BISPHOSPHATE 1BXNTHE CRYSTAL STRUCTURE OF RUBISCO FROM ALCALIGENES EUTROPHUS L YASE TO 2.7 ANGSTROMS. 1C17 A1C12 SUBCOMPLEX OF F1FO ATP SYNTHASE MEMBRANE PROTEIN 1C1Y CRYSTAL STRUCTURE OF RAP.GMPPNP IN COMPLEX WITH THE RAS- SIGNALING PROTEIN BINDING-DOMAIN OF C-RAF1 KINASE (RAFRBD). 1C3A CRYSTAL STRUCTURE OF FLAVOCETIN-A FROM THE HABU SNAKE VENOM, MEMBRANE PROTEIN A NOVEL CYCLIC TETRAMER OF C-TYPE LECTIN-LIKE HETERODIMERS 1C4Z STRUCTURE OF E6AP: INSIGHTS INTO UBIQUITINATION PATHWAY LIGASE 1C5C DECARBOXYLASE CATALYTIC ANTIBODY 21D8-HAPTEN COMPLEX IMMUNE SYSTEM 5 Supplementary Material (ESI) for Molecular BioSystems This journal is (c) The Royal Society of Chemistry, 2009 1C5D THE CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF A RAT IMMUNE SYSTEM MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR 1C5F CRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM ISOMERASE/IMMUNE SYSTEM BRUGIA MALAYI COMPLEXED WITH CYCLOSPORIN A 1C6V SIV INTEGRASE (CATALYTIC DOMAIN + DNA BIDING DOMAIN DNA BINDING PROTEIN COMPRISING RESIDUES 50-293) MUTANT WITH PHE 185 REPLACED BY HIS (F185H) 1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB TRANSCRIPTION/DNA CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) 1C9L PEPTIDE-IN-GROOVE INTERACTIONS LINK TARGET PROTEINS TO THE ENDOCYTOSIS/EXOCYTOSIS B-PROPELLER OF CLATHRIN 1CBV AN AUTOANTIBODY TO SINGLE-STRANDED DNA: COMPARISON OF THE IMMUNE SYSTEM/DNA THREE-DIMENSIONAL STRUCTURES OF THE UNLIGANDED FAB AND A DEOXYNUCLEOTIDE-FAB COMPLEX 1CC1 CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE OXIDOREDUCTASE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM 1CCWSTRUCTURE OF THE COENZYME B12 DEPENDENT ENZYME GLUTAMATE ISOMERASE MUTASE FROM CLOSTRIDIUM COCHLEARIUM 1CD3 PROCAPSID OF BACTERIOPHAGE PHIX174 VIRUS 1CD9 2:2 COMPLEX OF G-CSF WITH ITS RECEPTOR CYTOKINE 1CE7 MISTLETOE LECTIN I FROM VISCUM ALBUM RIBOSOME 1CF7 STRUCTURAL BASIS OF DNA RECOGNITION BY THE HETERODIMERIC TRANSCRIPTION/DNA CELL CYCLE TRANSCRIPTION FACTOR E2F-DP 1CF8 CONVERGENCE OF CATALYTIC ANTIBODY AND TERPENE CYCLASE CATALYTIC ANTIBODY MECHANISMS: POLYENE CYCLIZATION DIRECTED BY CARBOCATION-PI INTERACTIONS 1CG5 DEOXY FORM HEMOGLOBIN FROM DASYATIS AKAJEI OXYGEN TRANSPORT 1CGL STRUCTURE OF THE CATALYTIC DOMAIN OF FIBROBLAST COLLAGENASE METALLOPROTEASE COMPLEXED WITH AN INHIBITOR 1CI6 TRANSCRIPTION FACTOR ATF4-C/EBP BETA BZIP HETERODIMER TRANSCRIPTION 1CLVYELLOW MEAL WORM ALPHA-AMYLASE IN COMPLEX WITH THE AMARANTH H YDROLASE ALPHA-AMYLASE INHIBITOR 1CMI STRUCTURE OF THE HUMAN PIN/LC8 DIMER WITH A BOUND PEPTIDE OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 1CN3 INTERACTION OF POLYOMAVIRUS INTERNAL PROTEIN VP2 WITH MAJOR VIRAL PROTEIN CAPSID PROTEIN VP1 AND IMPLICATIONS FOR PARTICIPATION OF 6 Supplementary Material (ESI) for Molecular BioSystems This journal is (c) The Royal Society of Chemistry, 2009 VP2 IN VIRAL ENTRY 1CP9 CRYSTAL STRUCTURE OF PENICILLIN G ACYLASE FROM THE BRO1 HYDROLASE MUTANT STRAIN OF PROVIDENCIA RETTGERI 1CPC ISOLATION, CRYSTALLIZATION, CRYSTAL STRUCTURE ANALYSIS AND LIGHT HARVESTING PROTEIN REFINEMENT OF CONSTITUTIVE C-PHYCOCYANIN FROM THE CHROMATICALLY ADAPTING CYANOBACTERIUM FREMYELLA DIPLOSIPHON AT 1.66 ANGSTROMS RESOLUTION 1CQT CRYSTAL STRUCTURE OF A TERNARY COMPLEX CONTAINING AN OCA-B GENE REGULATION/DNA PEPTIDE, THE OCT-1 POU DOMAIN, AND AN OCTAMER ELEMENT 1CVU CRYSTAL STRUCTURE OF ARACHIDONIC ACID BOUND TO THE OXIDOREDUCTASE CYCLOOXYGENASE ACTIVE SITE OF COX-2 1CZQ CRYSTAL STRUCTURE OF THE D10-P1/IQN17 COMPLEX: A D-PEPTIDE VIRAL PROTEIN/VIRAL PROTEIN INHIBITOR INHIBITOR OF HIV-1 ENTRY BOUND TO THE GP41 COILED-COIL POCKET. 1CZYCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE TRAF DOMAIN OF A POPTOSIS HUMAN TRAF2 AND AN LMP1 BINDING PEPTIDE 1D2Z THREE-DIMENSIONAL STRUCTURE OF A COMPLEX BETWEEN THE DEATH APOPTOSIS DOMAINS OF PELLE AND TUBE 1D3B CRYSTAL STRUCTURE OF THE D3B SUBCOMPLEX OF THE HUMAN CORE RNA BINDING PROTEIN SNRNP DOMAIN AT 2.0A RESOLUTION 1D3U TATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/BRE+TATA- GENE REGULATION/DNA BOX COMPLEX FROM PYROCOCCUS WOESEI 1D4T CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP IN COMPLEX WITH A SIGNALING PROTEIN SLAM PEPTIDE 1D6G MOLECULAR COMPLEX OF CHOLECYSTOKININ-8 AND N-TERMINUS OF HORMONE/GROWTH FACTOR THE CHOLECYSTOKININ A RECEPTOR BY NMR SPECTROSCOPY 1DEV CRYSTAL STRUCTURE OF SMAD2 MH2 DOMAIN BOUND TO THE SMAD- SIGNALING PROTEIN BINDING DOMAIN OF SARA 1DKD CRYSTAL STRUCTURE OF A GROEL (APICAL DOMAIN) AND A CHAPERONE DODECAMERIC PEPTIDE COMPLEX 1DKG CRYSTAL STRUCTURE OF THE NUCLEOTIDE EXCHANGE FACTOR GRPE COMPLEX (HSP24/HSP70) BOUND TO THE ATPASE DOMAIN OF THE MOLECULAR CHAPERONE DNAK 1DKZ THE SUBSTRATE BINDING DOMAIN OF DNAK IN COMPLEX WITH A COMPLEX (MOLECULAR CHAPERONE/PEPTIDE) SUBSTRATE PEPTIDE, DETERMINED FROM TYPE 1 NATIVE CRYSTALS 1DML CRYSTAL STRUCTURE OF HERPES SIMPLEX UL42 BOUND TO THE C- DNA BINDING PROTEIN/TRANSFERASE TERMINUS OF HSV POL 1DN0 STRUCTURE OF THE FAB FRAGMENT FROM A HUMAN IGM COLD IMMUNE SYSTEM AGGLUTININ 7 Supplementary Material (ESI) for Molecular BioSystems This journal is (c) The Royal Society of Chemistry, 2009 1DNUSTRUCTURAL ANALYSES OF HUMAN MYELOPEROXIDASE-THIOCYANATE OXIDOREDUCTASE COMPLEX 1DOW CRYSTAL STRUCTURE OF A CHIMERA OF BETA-CATENIN AND ALPHA- CELL ADHESION CATENIN 1DPJ THE STRUCTURE OF PROTEINASE A COMPLEXED WITH IA3 PEPTIDE HYDROLASE/HYDROLASE INHIBITOR INHIBITOR 1DPP DIPEPTIDE BINDING PROTEIN COMPLEX WITH GLYCYL-L-LEUCINE COMPLEX (BINDING PROTEIN/PEPTIDE) 1DSZ STRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER IN TRANSCRIPTION/DNA COMPLEX WITH THE RETINOIC ACID RESPONSE ELEMENT DR1 1DTD CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE LEECH HYDROLASE/HYDROLASE INHIBITOR CARBOXYPEPTIDASE INHIBITOR AND THE HUMAN CARBOXYPEPTIDASE A2 (LCI-CPA2) 1DY9 INHIBITION OF THE HEPATITIS C VIRUS NS3/4A PROTEASE. THE SERINE PROTEASE CRYSTAL STRUCTURES OF TWO PROTEASE-INHIBITOR COMPLEXES (INHIBITOR I) 1E3D [NIFE] HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS ATCC HYDROGENASE 27774 RIBONUCLEASE DOMAIN OF COLICIN E3 IN COMPLEX WITH ITS RIBONUCLEASE IMMUNITY PROTEIN 1E4W CROSSREACTIVE BINDING OF A CIRCULARIZED PEPTIDE TO AN ANTI- COMPLEX (ANTIBODY/ANTIGEN) TGFALPHA ANTIBODY FAB-FRAGMENT AML1/CBF COMPLEX TRANSCRIPTION FACTOR 1E6EADRENODOXIN REDUCTASE/ADRENODOXIN COMPLEX OF MITOCHONDRIAL O XIDOREDUCTASE P450 SYSTEMS 1E6V METHYL-COENZYME M REDUCTASE FROM METHANOPYRUS KANDLERI OXIDOREDUCTASE 1E6Y METHYL-COENZYME M REDUCTASE FROM METHANOSARCINA BARKERI OXIDOREDUCTASE 1E8N PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, MUTANT, COMPLEXED HYDROLASE WITH PEPTIDE 1E8O CORE OF THE ALU DOMAIN OF THE MAMMALIAN SRP SIGNALING PROTEIN/RNA HSLV-HSLU FROM E.COLI CHAPERONE 1E9Z CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREASE HYDROLASE 1EAK CATALYTIC DOMAIN OF PROMMP-2 E404Q MUTANT HYDROLYSE 1EE4 CRYSTAL STRUCTURE OF YEAST KARYOPHERIN (IMPORTIN) ALPHA IN TRANSPORT PROTEIN A COMPLEX WITH A C-MYC NLS PEPTIDE 8 Supplementary Material (ESI) for Molecular BioSystems This journal is (c) The Royal Society of Chemistry, 2009 1EEO CRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B HYDROLASE COMPLEXED WITH ACETYL-E-L-E-F-PTYR-M-D-Y-E-NH2 1EER CRYSTAL STRUCTURE OF HUMAN ERYTHROPOIETIN COMPLEXED TO ITS COMPLEX (CYTOKINE/RECEPTOR) RECEPTOR AT 1.9 ANGSTROMS 1EF1 CRYSTAL STRUCTURE OF THE MOESIN FERM DOMAIN/TAIL DOMAIN MEMBRANE PROTEIN COMPLEX 1EFP ELECTRON TRANSFER FLAVOPROTEIN (ETF) FROM PARACOCCUS ELECTRON TRANSPORT DENITRIFICANS 1EFV THREE-DIMENSIONAL STRUCTURE OF HUMAN ELECTRON TRANSFER ELECTRON TRANSPORT FLAVOPROTEIN TO 2.1 A RESOLUTION 1EG4 STRUCTURE OF A DYSTROPHIN WW DOMAIN FRAGMENT IN COMPLEX STRUCTURAL PROTEIN WITH A BETA-DYSTROGLYCAN PEPTIDE 1EGJ DOMAIN 4 OF THE BETA COMMON CHAIN IN COMPLEX WITH AN IMMUNE SYSTEM ANTIBODY 1EGV CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE- LYASE ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSELLA OXYTOCA UNDER THE ILLUMINATED CONDITION. 1EHL 64M-2 ANTIBODY FAB COMPLEXED WITH D(5HT)(6-4)T IMMUNE SYSTEM 1EIY THE CRYSTAL STRUCTURE OF PHENYLALANYL-TRNA SYNTHETASE FROM L IGASE/RNA THERMUS THERMOPHILUS COMPLEXED WITH COGNATE TRNAPHE 1EJ6 REOVIRUS CORE VIRUS 1EJX CRYSTAL STRUCTURE OF WILD-TYPE KLEBSIELLA AEROGENES UREASE HYDROLASE AT 100K 1ELR CRYSTAL STRUCTURE OF THE TPR2A DOMAIN OF HOP IN COMPLEX CHAPERONE WITH THE HSP90 PEPTIDE MEEVD 1ELW CRYSTAL STRUCTURE OF THE TPR1 DOMAIN OF HOP IN COMPLEX WITH CHAPERONE A HSC70 PEPTIDE 1EM8 CRYSTAL STRUCTURE OF CHI AND PSI SUBUNIT HETERODIMER FROM GENE REGULATION DNA POL III 1EMUSTRUCTURE OF THE AXIN RGS-HOMOLOGOUS DOMAIN IN COMPLEX WITH SIGNALING PROTEIN A SAMP REPEAT FROM APC 1EP3 CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE OXIDOREDUCTASE DEHYDROGENASE B. DATA COLLECTED UNDER CRYOGENIC CONDITIONS. 1EQZ X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A STRUCTURAL PROTEIN/DNA RESOLUTION 1ES0 CRYSTAL STRUCTURE OF THE MURINE CLASS II ALLELE I-A(G7) IMMUNE SYSTEM COMPLEXED WITH THE GLUTAMIC ACID DECARBOXYLASE (GAD65) 9 Supplementary Material (ESI) for Molecular BioSystems This journal is (c) The Royal Society of Chemistry, 2009 PEPTIDE 207-220 1EUC CRYSTAL STRUCTURE OF DEPHOSPHORYLATED PIG HEART, GTP- LIGASE SPECIFIC SUCCINYL-COA SYNTHETASE 1EUV X-RAY STRUCTURE OF THE C-TERMINAL ULP1 PROTEASE DOMAIN IN HYDROLASE COMPLEX WITH SMT3, THE YEAST ORTHOLOG OF SUMO. 1EWP CRUZAIN BOUND TO MOR-LEU-HPQ HYDROLASE 1EWY ANABAENA PCC7119 FERREDOXIN:FERREDOXIN-NADP+-REDUCTASE OXIDOREDUCTASE COMPLEX 1EXB STRUCTURE OF THE CYTOPLASMIC BETA SUBUNIT-T1 ASSEMBLY OF METAL TRANSPORT VOLTAGE-DEPENDENT K CHANNELS 1EYS CRYSTAL STRUCTURE OF PHOTOSYNTHETIC REACTION CENTER FROM A ELECTRON TRANSPORT THERMOPHILIC BACTERIUM, THERMOCHROMATIUM TEPIDUM 1EYX CRYSTAL STRUCTURE OF R-PHYCOERYTHRIN AT 2.2 ANGSTROMS PHOTOSYNTHESIS 1F02 CRYSTAL STRUCTURE OF C-TERMINAL 282-RESIDUE FRAGMENT OF CELL ADHESION INTIMIN IN COMPLEX WITH TRANSLOCATED INTIMIN RECEPTOR (TIR) INTIMIN-BINDING DOMAIN 1F2R NMR STRUCTURE OF THE HETERODIMERIC COMPLEX BETWEEN CAD DNA BINDING PROTEIN DOMAINS OF CAD AND ICAD 1F2T CRYSTAL STRUCTURE OF ATP-FREE RAD50 ABC-ATPASE REPLICATION 1F3U CRYSTAL STRUCTURE OF THE RAP30/74 INTERACTION DOMAINS OF TRANSCRIPTION HUMAN TFIIF 1F47 THE BACTERIAL CELL-DIVISION PROTEIN ZIPA AND ITS CELL CYCLE INTERACTION WITH AN FTSZ FRAGMENT REVEALED BY X-RAY CRYSTALLOGRAPHY 1F51 A TRANSIENT INTERACTION BETWEEN TWO PHOSPHORELAY PROTEINS TRANSFERASE TRAPPED IN A CRYSTAL LATTICE REVEALS THE MECHANISM OF MOLECULAR RECOGNITION AND PHOSPHOTRANSFER IN SINGAL TRANSDUCTION 1F60 CRYSTAL STRUCTURE OF THE YEAST ELONGATION FACTOR COMPLEX TRANSLATION EEF1A:EEF1BA 1F66 2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE STRUCTURAL PROTEIN/DNA CONTAINING THE VARIANT HISTONE H2A.Z 1F6F CRYSTAL STRUCTURE OF THE TERNARY COMPLEX BETWEEN OVINE HORMONE/GROWTH FACTOR/HORMONE RECEPTOR PLACENTAL LACTOGEN AND THE EXTRACELLULAR DOMAIN OF THE RAT PROLACTIN RECEPTOR 1F80 HOLO-(ACYL CARRIER PROTEIN) SYNTHASE IN COMPLEX WITH HOLO- TRANSFERASE (ACYL CARRIER PROTEIN) 10