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(-) Description

Title :  COMPLEMENT COMPONENT C2A, THE CATALYTIC FRAGMENT OF C3- AND C5-CONVERTASE OF HUMAN COMPLEMENT
 
Authors :  S. V. L. Narayana, V. Krishnan
Date :  25 Dec 06  (Deposition) - 06 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Complement Component C2A, C3/C5 Convertase, Complement Serine Protease, Human Complement System, Glycoprotein, Sp, Vwfa, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Krishnan, Y. Xu, K. Macon, J. E. Volanakis, S. V. Narayana
The Crystal Structure Of C2A, The Catalytic Fragment Of Classical Pathway C3 And C5 Convertase Of Human Complement.
J. Mol. Biol. V. 367 224 2007
PubMed-ID: 17234210  |  Reference-DOI: 10.1016/J.JMB.2006.12.039

(-) Compounds

Molecule 1 - COMPLEMENT C2
    ChainsA
    EC Number3.4.21.43
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Cell LineHIGH FIVE(BTI-TN-5B1-4)
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    FragmentCOMPLEMENT C2A FRAGMENT
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymC3/C5 CONVERTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:532 , ASN A:631 , THR A:633 , NAG A:802 , NAG A:803BINDING SITE FOR RESIDUE NAG A 801
2AC2SOFTWAREGLN A:532 , NAG A:801 , NAG A:803BINDING SITE FOR RESIDUE NAG A 802
3AC3SOFTWAREGLN A:532 , NAG A:801 , NAG A:802BINDING SITE FOR RESIDUE NAG A 803
4AC4SOFTWARELYS A:224 , GLU A:430 , LEU A:433 , ASN A:447 , GLU A:456 , NAG A:805 , HOH A:955 , HOH A:956 , HOH A:981BINDING SITE FOR RESIDUE NAG A 804
5AC5SOFTWARELYS A:224 , HIS A:431 , ASP A:434 , NAG A:804 , NAG A:806 , HOH A:1043 , HOH A:1096 , HOH A:1098BINDING SITE FOR RESIDUE NAG A 805
6AC6SOFTWARENAG A:805 , HOH A:1067BINDING SITE FOR RESIDUE NAG A 806
7AC7SOFTWAREASN A:601 , SER A:603 , ASN A:692 , ARG A:694BINDING SITE FOR RESIDUE NAG A 807
8AC8SOFTWARELYS A:309 , GLU A:312 , ASN A:313 , LYS A:517BINDING SITE FOR RESIDUE NAG A 808
9AC9SOFTWARESER A:242 , SER A:244 , THR A:317 , HOH A:902 , HOH A:903 , HOH A:904BINDING SITE FOR RESIDUE MG A 901

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:443 -A:561
2A:472 -A:488
3A:564 -A:580
4A:618 -A:645
5A:655 -A:685

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:702 -Pro A:703

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_019158E318DCO2_HUMANPolymorphism9332739AE298D
2UniProtVAR_008546G464RCO2_HUMANDisease (C2D)151340617AG444R
3UniProtVAR_011772F533LCO2_HUMANPolymorphism1042664AF513L
4UniProtVAR_019159R734CCO2_HUMANPolymorphism4151648AR714C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VWFAPS50234 VWFA domain profile.CO2_HUMAN254-452  1A:234-432
2TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CO2_HUMAN464-744  1A:444-724
3TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CO2_HUMAN503-508  1A:483-488
4TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CO2_HUMAN673-684  1A:653-664

(-) Exons   (0, 0)

(no "Exon" information available for 2ODP)

(-) Sequences/Alignments

Asymmetric/Biological 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:490
 aligned with CO2_HUMAN | P06681 from UniProtKB/Swiss-Prot  Length:752

    Alignment length:507
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       
            CO2_HUMAN   244 KIQIQRSGHLNLYLLLDCSQSVSENDFLIFKESASLMVDRIFSFEINVSVAIITFASEPKVLMSVLNDNSRDMTEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGMETMAWQEIRHAIILLTDGKSNMGGSPKTAVDHIREILNINQKRNDYLDIYAIGVGKLDVDWRELNELGSKKDGERHAFILQDTKALHQVFEHMLDVSKLTDTICGVGNMSANASDQERTPWHVTIKPKSQETCRGALISDQWVLTAAHCFRDGNDHSLWRVNVGDPKSQWGKEFLIEKAVISPGFDVFAKKNQGILEFYGDDIALLKLAQKVKMSTHARPICLPCTMEANLALRRPQGSTCRDHENELLNKQSVPAHFVALNGSKLNINLKMGVEWTSCAEVVSQEKTMFPNLTDVREVVTDQFLCSGTQEDESPCKGESGGAVFLERRFRFFQVGLVSWGLYNPCLGSADKNSRKRAPRSKVPPPRDFHINLFRMQPWLRQHLGDVLNFL 750
               SCOP domains d2odpa1 A:224-442 automated matches                                                                                                                                                                                        d2odpa2 A:443-730 automa    ted matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------VWA-2odpA02 A:234-432                                                                                                                                                                                  -------------Trypsin-2odpA01 A:446    -686                                                                                                                                                                                                                         --------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh....eeeeeeee...eeeee...hhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhhhhhh..hhhhhheeeeeeee..........hhhhhhhhhhhh.....hhh.eeeeeeee.....hhhhhhhhh........eeee.hhhhhhhhhhhhee..................hhhhhh..eeeee.----.eeeee....eeeehhhhh--------.eeee........eee.eeeeee........hhhhh.........eeeee.................hhhhhhhh......hhhhhhhhhh...eeeeeee.....eeeeeee.hhhhhhhhhhhhhh........hhhhh....eeee........hhhhh..eeeeee..eeeeeeeeeee......-----...............eeeee...hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------D-------------------------------------------------------------------------------------------------------------------------------------------------R--------------------------------------------------------------------L--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C---------------- SAPs(SNPs)
                PROSITE (1) ----------VWFA  PDB: A:234-432 UniProt: 254-452                                                                                                                                                                  -----------TRYPSIN_DOM  PDB: A:444-724 UniProt: 464-744                                                                                                                                                                                                                                             ------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSI--------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2odp A 224 KIQIQRSGHLNLYLLLDASQSVSENDFLIFKESASLMVDRIFSFEINVSVAIITFASEPKVLMSVLNDNSRDMTEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGMETMAWQEIRHAIILLTDGKSNMGGSPKTAVDHIREILNINQKRNDYLDIYAIGVGKLDVDWRELNELGSKKDGERHAFILQDTKALHQVFEHMLDVSKLTDTICGVGNMSANASDQERTPWHVTIKP----TCRGALISDQWVLTAAHCF--------WRVNVGDPKSQWGKEFLIEKAVISPGFDVFAKKNQGILEFYGDDIALLKLAQKVKMSTHARPICLPCTMEANLALRRPQGSTCRDHENELLNKQSVPAHFVALNGSKLNINLKMGVEWTSCAEVVSQEKTMFPNLTDVREVVTDQFLCSGTQEDESPCKGESGGAVFLERRFRFFQVGLVSWGLYNPCL-----NSRKRAPRSKVPPPRDFHINLFRMQPWLRQHLGDVLNFL 730
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463  |    473       483     |   -    |  503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683  |    693       703       713       723       
                                                                                                                                                                                                                                                                            466  471               489      498                                                                                                                                                                                         686   692                                      

Chain A from PDB  Type:PROTEIN  Length:490
 aligned with Q53HP3_HUMAN | Q53HP3 from UniProtKB/TrEMBL  Length:752

    Alignment length:507
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       
         Q53HP3_HUMAN   244 KIQIQRSGHLNLYLLLDCSQSVSENDFLIFKESASLMVDRIFSFEINVSVAIITFASEPKVLMSVLNDNSRDMTEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGMETMAWQEIRHAIILLTDGKSNMGGSPKTAVDHIREILNINQKRNDYLDIYAIGVGKLDVDWRELNELGSKKDGERHAFILQDTKALHQVFEHMLDVSKLTDTICGVGNMSANASDQERTPWHVTIKPKSQETCRGALISDQWVLTAAHCFRDGNDHSLWRVNVGDPKSQWGKEFLIEKAVISPGFDVFAKKNQGILEFYGDDIALLKLAQKVKMSTHARPICLPCTMEANLALRRPQGSTCRDHENELLNKQSVPAHFVALNGSKLNINLKMGVEWTSCAEVVSQEKTMFPNLTDVREVVTDQFLCSGTQEDESPCKGESGGAVFLERRFRFFQVGLVSWGLYNPCLGSADKNSRKRAPRSKVPPPRDFHINLFRMQPWLRQHLGDVLNFL 750
               SCOP domains d2odpa1 A:224-442 automated matches                                                                                                                                                                                        d2odpa2 A:443-730 automa    ted matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------VWA-2odpA02 A:234-432                                                                                                                                                                                  -------------Trypsin-2odpA01 A:446    -686                                                                                                                                                                                                                         --------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh....eeeeeeee...eeeee...hhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhhhhhh..hhhhhheeeeeeee..........hhhhhhhhhhhh.....hhh.eeeeeeee.....hhhhhhhhh........eeee.hhhhhhhhhhhhee..................hhhhhh..eeeee.----.eeeee....eeeehhhhh--------.eeee........eee.eeeeee........hhhhh.........eeeee.................hhhhhhhh......hhhhhhhhhh...eeeeeee.....eeeeeee.hhhhhhhhhhhhhh........hhhhh....eeee........hhhhh..eeeeee..eeeeeeeeeee......-----...............eeeee...hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------D-------------------------------------------------------------------------------------------------------------------------------------------------R--------------------------------------------------------------------L--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C---------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2odp A 224 KIQIQRSGHLNLYLLLDASQSVSENDFLIFKESASLMVDRIFSFEINVSVAIITFASEPKVLMSVLNDNSRDMTEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGMETMAWQEIRHAIILLTDGKSNMGGSPKTAVDHIREILNINQKRNDYLDIYAIGVGKLDVDWRELNELGSKKDGERHAFILQDTKALHQVFEHMLDVSKLTDTICGVGNMSANASDQERTPWHVTIKP----TCRGALISDQWVLTAAHCF--------WRVNVGDPKSQWGKEFLIEKAVISPGFDVFAKKNQGILEFYGDDIALLKLAQKVKMSTHARPICLPCTMEANLALRRPQGSTCRDHENELLNKQSVPAHFVALNGSKLNINLKMGVEWTSCAEVVSQEKTMFPNLTDVREVVTDQFLCSGTQEDESPCKGESGGAVFLERRFRFFQVGLVSWGLYNPCL-----NSRKRAPRSKVPPPRDFHINLFRMQPWLRQHLGDVLNFL 730
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463  |    473       483     |   -    |  503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683  |    693       703       713       723       
                                                                                                                                                                                                                                                                            466  471               489      498                                                                                                                                                                                         686   692                                      

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ODP)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: vWA-like (60)
(-)
Family: VWA (50)

(-) Gene Ontology  (16, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q53HP3_HUMAN | Q53HP3)
molecular function
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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).
biological process
    GO:0006956    complement activation    Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain A   (CO2_HUMAN | P06681)
molecular function
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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).
biological process
    GO:0006956    complement activation    Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
    GO:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:2000427    positive regulation of apoptotic cell clearance    Any process that activates or increases the frequency, rate or extent of apoptotic cell clearance.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0030449    regulation of complement activation    Any process that modulates the frequency, rate or extent of complement activation.
    GO:0007584    response to nutrient    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CO2_HUMAN | P066812i6q 2i6s 2odq 3erb
UniProtKB/TrEMBL
        Q53HP3_HUMAN | Q53HP32i6q

(-) Related Entries Specified in the PDB File

2odq THE SAME PROTEIN WITHOUT MG ION