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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE ZYMOGEN CATALYTIC DOMAIN OF COMPLEMENT PROTEASE C1R
 
Authors :  M. Budayova-Spano, J. C. Fontecilla-Camps, C. Gaboriaud
Date :  15 Nov 01  (Deposition) - 31 Jul 02  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Activation, Complement, Innate Immunity, Modular Structure, Serine Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Budayova-Spano, M. Lacroix, N. Thielens, G. Arlaud, J. C. Fontecilla-Camps, C. Gaboriaud
The Crystal Structure Of The Zymogen Catalytic Domain Of Complement Protease C1R Reveals That A Disruptive Mechanica Stress Is Required To Trigger Activation Of The C1 Complex.
Embo J. V. 21 231 2002
PubMed-ID: 11823416  |  Reference-DOI: 10.1093/EMBOJ/21.3.231

(-) Compounds

Molecule 1 - COMPLEMENT C1R COMPONENT
    ChainsA, B
    EC Number3.4.21.41
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Cell LineHIGH FIVE INSECT CELLS
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    FragmentCATALYTIC DOMAIN OF HUMAN C1R, RESIDUES 307-705
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsEXPRESSION USING A BACULOVIRUS/INSECT CELLS SYSTEM
    SynonymC1R COMPLEMENT SERINE PROTEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2MAN1Ligand/IonALPHA-D-MANNOSE
3NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2MAN-1Ligand/IonALPHA-D-MANNOSE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2MAN1Ligand/IonALPHA-D-MANNOSE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:295 , HIS A:335 , ASN A:367 , HIS A:390 , TYR A:394 , ASN A:564 , THR A:566 , PHE A:567 , ASP A:645 , PRO A:646 , ASN A:647BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 564 RESIDUES 2001 TO 2003
2AC2SOFTWAREILE A:304 , GLN A:305 , ASN A:306 , LEU A:307 , GLN B:495 , SER B:496 , ASN B:497 , ALA B:498 , SER B:499BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 497 RESIDUES 1001 TO 1004
3AC3SOFTWAREASN B:564BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 564 RESIDUES 3001 TO 3001

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:292 -A:341
2A:321 -A:354
3A:359 -A:412
4A:389 -A:430
5A:434 -A:560
6A:603 -A:622
7A:633 -A:663
8B:292 -B:341
9B:321 -B:354
10B:359 -B:412
11B:389 -B:430
12B:434 -B:560
13B:603 -B:622
14B:633 -B:663

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:391 -Pro A:392
2Glu B:391 -Pro B:392

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 12)

Asymmetric Unit (6, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_077113C309WC1R_HUMANDisease (EDSPD1)  ---A/BC292W
2UniProtVAR_077114C338RC1R_HUMANDisease (EDSPD1)  ---A/BC321R
3UniProtVAR_077115C358FC1R_HUMANDisease (EDSPD1)  ---A/BC341F
4UniProtVAR_077116W364CC1R_HUMANUnclassified (EDSPD1)  ---A/BW347C
5UniProtVAR_077117C371WC1R_HUMANDisease (EDSPD1)  ---A/BC354W
6UniProtVAR_077119W435RC1R_HUMANUnclassified (EDSPD1)  ---A/BW418R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_077113C309WC1R_HUMANDisease (EDSPD1)  ---AC292W
2UniProtVAR_077114C338RC1R_HUMANDisease (EDSPD1)  ---AC321R
3UniProtVAR_077115C358FC1R_HUMANDisease (EDSPD1)  ---AC341F
4UniProtVAR_077116W364CC1R_HUMANUnclassified (EDSPD1)  ---AW347C
5UniProtVAR_077117C371WC1R_HUMANDisease (EDSPD1)  ---AC354W
6UniProtVAR_077119W435RC1R_HUMANUnclassified (EDSPD1)  ---AW418R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_077113C309WC1R_HUMANDisease (EDSPD1)  ---BC292W
2UniProtVAR_077114C338RC1R_HUMANDisease (EDSPD1)  ---BC321R
3UniProtVAR_077115C358FC1R_HUMANDisease (EDSPD1)  ---BC341F
4UniProtVAR_077116W364CC1R_HUMANUnclassified (EDSPD1)  ---BW347C
5UniProtVAR_077117C371WC1R_HUMANDisease (EDSPD1)  ---BC354W
6UniProtVAR_077119W435RC1R_HUMANUnclassified (EDSPD1)  ---BW418R

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

(-) PROSITE Motifs  (3, 8)

Asymmetric Unit (3, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUSHIPS50923 Sushi/CCP/SCR domain profile.C1R_HUMAN307-373
 
374-449
 
  4A:290-356
B:290-356
A:357-432
B:357-432
2TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.C1R_HUMAN464-702
 
  2A:447-685
B:447-685
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.C1R_HUMAN648-659
 
  2A:631-642
B:631-642
Biological Unit 1 (3, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUSHIPS50923 Sushi/CCP/SCR domain profile.C1R_HUMAN307-373
 
374-449
 
  2A:290-356
-
A:357-432
-
2TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.C1R_HUMAN464-702
 
  1A:447-685
-
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.C1R_HUMAN648-659
 
  1A:631-642
-
Biological Unit 2 (3, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUSHIPS50923 Sushi/CCP/SCR domain profile.C1R_HUMAN307-373
 
374-449
 
  2-
B:290-356
-
B:357-432
2TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.C1R_HUMAN464-702
 
  1-
B:447-685
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.C1R_HUMAN648-659
 
  1-
B:631-642

(-) Exons   (0, 0)

(no "Exon" information available for 1GPZ)

(-) 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:369
 aligned with C1R_HUMAN | P00736 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:397
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       
            C1R_HUMAN   307 IKCPQPKTLDEFTIIQNLQPQYQFRDYFIATCKQGYQLIEGNQVLHSFTAVCQDDGTWHRAMPRCKIKDCGQPRNLPNGDFRYTTTMGVNTYKARIQYYCHEPYYKMQTRAGSRESEQGVYTCTAQGIWKNEQKGEKIPRCLPVCGKPVNPVEQRQRIIGGQKAKMGNFPWQVFTNIHGRGGGALLGDRWILTAAHTLYPKEHEAQSNASLDVFLGHTNVEELMKLGNHPIRRVSVHPDYRQDESYNFEGDIALLELENSVTLGPNLLPICLPDNDTFYDLGLMGYVSGFGVMEEKIAHDLRFVRLPVANPQACENWLRGKNRMDVFSQNMFCAGHPSLKQDACQGDSGGVFAVRDPNTDRWVATGIVSWGIGCSRGYGFYTKVLNYVDWIKKEMEE 703
               SCOP domains d1gpza2 A:290-357 Complement C1R protease domains                   d1gpza3 A:358-433 Complement C1R protease        domains                    d1gpza1 A:434-685 Complement C1R protease, catalytic domain                                                                                                                                                                                                 - SCOP domains
               CATH domains -------------------------------------------------------------------1gpzA04 A:357-433 Complement Module, domai       n 1                         --------1gpzA02 A:442-460  1gpzA01 A:461-558,A:676-681 Tryp     sin-like serine proteases                                    -1gpzA03 A:560-675 Try     psin-like serine pro           teases                                                     1gpzA0----- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee..........eeeeee...eeee....ee..eeee............eeee...........eeeee...........eeeeee....eeee.-------...eeee.....eee........eeee..................ee........eeeee...eeeeeee...eeeehhhhh.....-----...eeee...hhhhhhhh....eeeeee................eeeee.................hhhhhh...eeeeee..-----.....eeeeeeeehhhhhhh-----------...eeeee.hhhhhhhhh.....eeeeee....eeeeeeee.........eeeeee...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --W----------------------------R-------------------F-----C------W---------------------------------------------------------------R---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) SUSHI  PDB: A:290-356 UniProt: 307-373                             SUSHI  PDB: A:357-432 UniProt: 374-449                                      --------------TRYPSIN_DOM  PDB: A:447-685 UniProt: 464-702                                                                                                                                                                                                   - PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gpz A 290 IKCPQPKTLDEFTIIQNLQPQYQFRDYFIATCKQGYQLIEGNQVLHSFTAVCQDDGTWHRAMPRCKIKDCGQPRNLPNGDFRYTTTMGVNTYKARIQYYCHEPYYKMQT-------EQGVYTCTAQGIWKNEQKGEKIPRCLPVCGKPVNPVEQRQQIIGGQKAKMGNFPWQVFTNIHGRGGGALLGDRWILTAAHTLYPKEH-----ASLDVFLGHTNVEELMKLGNHPIRRVSVHPDYRQDESYNFEGDIALLELENSVTLGPNLLPICLPDNDTFYDLGLMGYVSGFG-----IAHDLRFVRLPVANPQACEN-----------SQNMFCAGHPSLKQDACQGDSGGVFAVRDPNTDRWVATGIVSWGIGCSRGYGFYTKVLNYVDWIKKEMEE 686
                                   299       309       319       329       339       349       359       369       379       389        |-      |409       419       429       439       449       459       469       479       489  |    499       509       519       529       539       549       559       569       579|     |589       599     |   -       619       629       639       649       659       669       679       
                                                                                                                                      398     406                                                                                   492   498                                                                               580   586                605         617                                                                     

Chain B from PDB  Type:PROTEIN  Length:368
 aligned with C1R_HUMAN | P00736 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:397
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       
            C1R_HUMAN   307 IKCPQPKTLDEFTIIQNLQPQYQFRDYFIATCKQGYQLIEGNQVLHSFTAVCQDDGTWHRAMPRCKIKDCGQPRNLPNGDFRYTTTMGVNTYKARIQYYCHEPYYKMQTRAGSRESEQGVYTCTAQGIWKNEQKGEKIPRCLPVCGKPVNPVEQRQRIIGGQKAKMGNFPWQVFTNIHGRGGGALLGDRWILTAAHTLYPKEHEAQSNASLDVFLGHTNVEELMKLGNHPIRRVSVHPDYRQDESYNFEGDIALLELENSVTLGPNLLPICLPDNDTFYDLGLMGYVSGFGVMEEKIAHDLRFVRLPVANPQACENWLRGKNRMDVFSQNMFCAGHPSLKQDACQGDSGGVFAVRDPNTDRWVATGIVSWGIGCSRGYGFYTKVLNYVDWIKKEMEE 703
               SCOP domains d1gpzb2 B:290-357 Complement C1R protease domains                   d1gpzb3 B:358-433 Complement C1R protease          domains                  d1gpzb1 B:434-685 Complement C1R protease, catalytic domain                                                                                                                                                                                                 - SCOP domains
               CATH domains -------------------------------------------------------------------1gpzB04 B:357-433 Complement Module, domai         n 1                       --------1gpzB02 B:442-460  1gpzB01 B:461-558,B:676-681 Tryp  sin-like serine proteases                                       -1gpzB03 B:560-675 Try     psin-like serine pr             oteases                                                   1gpzB0----- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.........eee......ee...eeeeee...eeeee..eee..eeee............eeee...........eeeee...........eeeeee....eee..---------.eeee.....ee..........eee...............eeeee........eeeee...eeeeeee...eeeehhhhh.....--......eeee...hhhhhhhh....eeeeee................eeeee..........................eeeeee..-----.....eeeeeeeehhhhh.-------------..eeeee.hhhhhhhhhh....eeeee......eeeeeee.........eeeeee...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --W----------------------------R-------------------F-----C------W---------------------------------------------------------------R---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) SUSHI  PDB: B:290-356 UniProt: 307-373                             SUSHI  PDB: B:357-432 UniProt: 374-449                                      --------------TRYPSIN_DOM  PDB: B:447-685 UniProt: 464-702                                                                                                                                                                                                   - PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gpz B 290 IKCPQPKTLDEFTIIQNLQPQYQFRDYFIATCKQGYQLIEGNQVLHSFTAVCQDDGTWHRAMPRCKIKDCGQPRNLPNGDFRYTTTMGVNTYKARIQYYCHEPYYKMQT---------GVYTCTAQGIWKNEQKGEKIPRCLPVCGKPVNPVEQRQQIIGGQKAKMGNFPWQVFTNIHGRGGGALLGDRWILTAAHTLYPKEH--QSNASLDVFLGHTNVEELMKLGNHPIRRVSVHPDYRQDESYNFEGDIALLELENSVTLGPNLLPICLPDNDTFYDLGLMGYVSGFG-----IAHDLRFVRLPVANPQACE-------------QNMFCAGHPSLKQDACQGDSGGVFAVRDPNTDRWVATGIVSWGIGCSRGYGFYTKVLNYVDWIKKEMEE 686
                                   299       309       319       329       339       349       359       369       379       389        |-       409       419       429       439       449       459       469       479       489  |  | 499       509       519       529       539       549       559       569       579|     |589       599    |    -       619       629       639       649       659       669       679       
                                                                                                                                      398       408                                                                                 492  |                                                                                  580   586               604           618                                                                    
                                                                                                                                                                                                                                       495                                                                                                                                                                                               

   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, 6)

Asymmetric Unit

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GPZ)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (C1R_HUMAN | P00736)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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: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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        C1R_HUMAN | P007361apq 1md7 1md8 2qy0

(-) Related Entries Specified in the PDB File

1apq STRUCTURE OF THE EGF-LIKE MODULE OF HUMAN C1R, NMR, 19 STRUCTURES
1elv STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COMPLEMENT C1S PROTEASE