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(-) Description

Title :  HCV NS3 PROTEASE DOMAIN WITH P1-P3 MACROCYCLIC KETOAMIDE INHIBITOR
 
Authors :  S. Venkatraman, F. Velazquez, W. Wu, M. Blackman, K. X. Chen, S. Bogen, L X. Tong, R. Chase, A. Hart, S. Agrawal, J. Pichardo, A. Prongay, K. -C. C V. Girijavallabhan, J. Piwinski, N. -Y. Shih, F. G. Njoroge
Date :  12 Nov 09  (Deposition) - 27 Oct 10  (Release) - 27 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hepatitis C Virus, Ns3 Protease Domain, Serine Protease, Macrocyclic Ketoamide Inhibitor, Atp-Binding, Envelope Protein, Helicase, Hydrolase, Membrane, Nucleotide-Binding, Rna Replication, Transmembrane, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Venkatraman, F. Velazquez, W. Wu, M. Blackman, K. X. Chen, S. Bogen, L. Nair, X. Tong, R. Chase, A. Hart, S. Agrawal, J. Pichardo, A. Prongay K. C. Cheng, V. Girijavallabhan, J. Piwinski, N. Y. Shih, F. G. Njoroge
Discovery And Structure-Activity Relationship Of P1-P3 Ketoamide Derived Macrocyclic Inhibitors Of Hepatitis C Virus Ns3 Protease.
J. Med. Chem. V. 52 336 2009
PubMed-ID: 19102654  |  Reference-DOI: 10.1021/JM800940U

(-) Compounds

Molecule 1 - HCV NS3 PROTEASE
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePET-3A
    FragmentPROTEASE DOMAIN, UNP RESIDUES 1027-1207
    GeneNS3
    Organism ScientificHEPATITIS C VIRUS SUBTYPE 1A
    Organism Taxid63746
    StrainH77 STRAIN OF GENOTYPE 1A
 
Molecule 2 - HCV NS4A PEPTIDE
    ChainsB, D
    EngineeredYES
    FragmentUNP RESIDUES 1678-1696
    MutationYES
    Other DetailsPEPTIDES WERE SYNTHESIZED USING FMOC SOLID-PHASE CHEMISTRY ON AN ABI 431 SYNTHESIZER (FOSTER CITY, CA). PRELOADED 2- CHLOROTRITYL CHLORIDE RESIN OR WANG RESIN WAS USED FOR THE SOLID PHASE ASSEMBLY OF NS4A ACTIVATOR PEPTIDE. THE SEQUENCE OF THE PEPTIDE WAS LYS-LYS-GLY-SER-VAL-VAL-ILE-VAL-GLY-ARG-ILE-ILE-LEU-SER- GLY-ARG-PRO-ALA-ILE-VAL-PRO-LYS-LYS-OH. TRIFUNCTIONAL RESIDUE SIDECHAIN PROTECTING GROUPS INCLUDED TERT-BUTYL FOR SER, TERT- BUTOXYCARBONYL FOR LYS, AND 2,2,4,6,7-PENTAMETHYLDIHYDROBENZOFURAN- 5-SULFONYL FOR ARG. CLEAVAGE AND SIDECHAIN DEPROTECTION WAS ACCOMPLISHED USING 92.5% TRIFLUOROACETIC ACID, WITH 2.5% EACH OF WATER, ETHANEDITHIOL AND TRIISOPROPYLSILANE FOR 2 HOURS. THE PEPTIDE WAS PURIFIED BY REVERSED PHASE HPLC. THE PEPTIDE MOLECULAR WEIGHT WAS CONFIRMED BY ELECTROSPRAY IONIZATION MASS SPECTROMETRY.
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2JZT1Ligand/Ion(2R)-2-{(3S,13S,16AS,17AR,17BS)-13-[({(1S)-1-[(4,4-DIMETHYL-2,6-DIOXOPIPERIDIN-1-YL)METHYL]-2,2-DIMETHYLPROPYL}CARBAMOYL)AMINO]-17,17-DIMETHYL-1,14-DIOXOOCTADECAHYDRO-2H-CYCLOPROPA[3,4]PYRROLO[1,2-A][1,4]DIAZACYCLOHEXADECIN-3-YL}-2-HYDROXY-N-PROP-2-EN-1-YLETHANAMIDE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2JZT1Ligand/Ion(2R)-2-{(3S,13S,16AS,17AR,17BS)-13-[({(1S)-1-[(4,4-DIMETHYL-2,6-DIOXOPIPERIDIN-1-YL)METHYL]-2,2-DIMETHYLPROPYL}CARBAMOYL)AMINO]-17,17-DIMETHYL-1,14-DIOXOOCTADECAHYDRO-2H-CYCLOPROPA[3,4]PYRROLO[1,2-A][1,4]DIAZACYCLOHEXADECIN-3-YL}-2-HYDROXY-N-PROP-2-EN-1-YLETHANAMIDE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1BME-1Ligand/IonBETA-MERCAPTOETHANOL
2JZT-1Ligand/Ion(2R)-2-{(3S,13S,16AS,17AR,17BS)-13-[({(1S)-1-[(4,4-DIMETHYL-2,6-DIOXOPIPERIDIN-1-YL)METHYL]-2,2-DIMETHYLPROPYL}CARBAMOYL)AMINO]-17,17-DIMETHYL-1,14-DIOXOOCTADECAHYDRO-2H-CYCLOPROPA[3,4]PYRROLO[1,2-A][1,4]DIAZACYCLOHEXADECIN-3-YL}-2-HYDROXY-N-PROP-2-EN-1-YLETHANAMIDE
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:97 , THR A:98 , CYS A:99 , CYS A:145 , HOH A:197BINDING SITE FOR RESIDUE ZN A 901
2AC2SOFTWAREGLN A:41 , THR A:42 , HIS A:57 , ARG A:123 , ILE A:132 , GLY A:137 , SER A:138 , SER A:139 , PHE A:154 , ARG A:155 , ALA A:156 , ALA A:157 , VAL A:158 , CYS A:159 , ASP A:168 , HOH A:219 , HOH A:240BINDING SITE FOR RESIDUE JZT A 999
3AC3SOFTWARECYS A:16 , ILE A:17 , THR A:38 , ALA A:39BINDING SITE FOR RESIDUE BME A 998
4AC4SOFTWARECYS C:97 , CYS C:99 , CYS C:145 , HOH C:190BINDING SITE FOR RESIDUE ZN C 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KNX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KNX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KNX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KNX)

(-) Exons   (0, 0)

(no "Exon" information available for 3KNX)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:181
 aligned with Q9ELS8_9HEPC | Q9ELS8 from UniProtKB/TrEMBL  Length:3011

    Alignment length:181
                                  1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206 
        Q9ELS8_9HEPC   1027 APITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRQGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTMRS 1207
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhh.........eeeee....eeeeeee..eeeeehhhhh...eee..eee...eee....eeeee................eeeee.....eeeeee....eeeeeeeeehhhhh.....eee.....eeeeeeeeeee..eeeeeeeeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3knx A    1 APITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTMRS  181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 

Chain B from PDB  Type:PROTEIN  Length:22
 aligned with Q9ELS8_9HEPC | Q9ELS8 from UniProtKB/TrEMBL  Length:3011

    Alignment length:22
                                  1686      1696  
        Q9ELS8_9HEPC   1677 TGCVVIVGRIVLSGKPAIIPDR 1698
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....eee... Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                3knx B   20 KGSVVIVGRIVLSGKPAIIPKK   41
                                    29        39  

Chain C from PDB  Type:PROTEIN  Length:151
 aligned with Q9ELS8_9HEPC | Q9ELS8 from UniProtKB/TrEMBL  Length:3011

    Alignment length:151
                                  1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204 
        Q9ELS8_9HEPC   1055 VEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRQGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTM 1205
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Peptidase_S29-3knxC01 C:30-178                                                                                                                       - Pfam domains (1)
           Pfam domains (2) -Peptidase_S29-3knxC02 C:30-178                                                                                                                       - Pfam domains (2)
         Sec.struct. author ....eeeee....eeeeeee..eeeeehhhhh..ee..........eee....eeeee................eeeee.....eeeeeeee..eeeeeeeee.hhhh.....eee.....eeeeeeeeee...eeeeeeeeehhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3knx C   29 VEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTM  179
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178 

Chain D from PDB  Type:PROTEIN  Length:16
 aligned with Q9ELS8_9HEPC | Q9ELS8 from UniProtKB/TrEMBL  Length:3011

    Alignment length:16
                                  1687      
        Q9ELS8_9HEPC   1678 GCVVIVGRIVLSGKPA 1693
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
           Pfam domains (1) --HCV_NS4a-3knxD Pfam domains (1)
           Pfam domains (2) --HCV_NS4a-3knxD Pfam domains (2)
         Sec.struct. author .eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                3knx D   21 GSVVIVGRIVLSGKPA   36
                                    30      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3KNX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KNX)

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9ELS8_9HEPC | Q9ELS8)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008026    ATP-dependent helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0017111    nucleoside-triphosphatase activity    Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0039520    induction by virus of host autophagy    Any process in which a virus activates or increases the frequency, rate or extent of autophagy in the host.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0019087    transformation of host cell by virus    Any virus-induced change in the morphological, biochemical, or growth parameters of a cell.
    GO:0039694    viral RNA genome replication    The replication of a viral RNA genome.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        Q9ELS8_9HEPC | Q9ELS82o8m 2obq 2oc0 2oc1 2oc7 2oc8 2oin 3eyd 3kn2
UniProtKB/TrEMBL
        Q9ELS8_9HEPC | Q9ELS82fm2 3lon 3lox

(-) Related Entries Specified in the PDB File

3eyd