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(-) Description

Title :  ACTIVE DIMERIC STRUCTURE OF THE CATALYTIC DOMAIN OF C1R REVEALS ENZYME-PRODUCT LIKE CONTACTS
 
Authors :  J. Kardos, V. Harmat, A. Pallo, O. Barabas, K. Szilagyi, L. Graf, G. Nara Y. Goto, P. Zavodszky, P. Gal
Date :  13 Aug 07  (Deposition) - 05 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Complement, Serine Protease, Beta Barrel, Complement Pathway, Egf- Like Domain, Glycoprotein, Hydrolase, Hydroxylation, Immune Response, Innate Immunity, Phosphorylation, Sushi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Kardos, V. Harmat, A. Pallo, O. Barabas, K. Szilagyi, L. Graf, G. Naray-Szabo, Y. Goto, P. Zavodszky, P. Gal
Revisiting The Mechanism Of The Autoactivation Of The Complement Protease C1R In The C1 Complex: Structure Of The Active Catalytic Region Of C1R.
Mol. Immunol. V. 45 1752 2008
PubMed-ID: 17996945  |  Reference-DOI: 10.1016/J.MOLIMM.2007.09.031

(-) Compounds

Molecule 1 - COMPLEMENT C1R SUBCOMPONENT
    ChainsA, C
    EC Number3.4.21.41
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-17B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSUSHI-1 AND SUSHI-2 DOMAINS, CCP1-CCP2
    GeneC1R
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - COMPLEMENT C1R SUBCOMPONENT
    ChainsB, D
    EC Number3.4.21.41
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-17B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPEPTIDASE S1 DOMAIN
    GeneC1R
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:159 , THR A:320 , TYR A:325 , LEU A:327 , LEU A:334 , LYS A:357BINDING SITE FOR RESIDUE GOL A 806
2AC2SOFTWARELEU B:475 , GLY B:476 , PRO B:558 , ILE B:559 , LEU B:561BINDING SITE FOR RESIDUE GOL B 801
3AC3SOFTWAREMET B:613 , ASN D:605 , GLY D:609BINDING SITE FOR RESIDUE GOL B 804
4AC4SOFTWAREASP C:315 , TYR C:316BINDING SITE FOR RESIDUE GOL C 802
5AC5SOFTWARETHR C:320 , CYS C:321 , TYR C:325 , LEU C:327 , LEU C:334 , HIS C:335BINDING SITE FOR RESIDUE GOL C 805
6AC6SOFTWAREGLY D:476 , ILE D:559BINDING SITE FOR RESIDUE GOL D 800
7AC7SOFTWAREASN B:605 , ARG B:608 , GLY B:609 , HOH D:37 , MET D:613BINDING SITE FOR RESIDUE GOL D 803

(-) SS Bonds  (14, 14)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Glu A:391 -Pro A:392
2Glu C:391 -Pro C:392
3Ser C:405 -Glu C:406

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 12)

Asymmetric/Biological Unit (6, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_077113C309WC1R_HUMANDisease (EDSPD1)  ---A/CC292W
2UniProtVAR_077114C338RC1R_HUMANDisease (EDSPD1)  ---A/CC321R
3UniProtVAR_077115C358FC1R_HUMANDisease (EDSPD1)  ---A/CC341F
4UniProtVAR_077116W364CC1R_HUMANUnclassified (EDSPD1)  ---A/CW347C
5UniProtVAR_077117C371WC1R_HUMANDisease (EDSPD1)  ---A/CC354W
6UniProtVAR_077119W435RC1R_HUMANUnclassified (EDSPD1)  ---A/CW418R

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

(-) PROSITE Motifs  (3, 8)

Asymmetric/Biological Unit (3, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUSHIPS50923 Sushi/CCP/SCR domain profile.C1R_HUMAN307-373
 
374-449
 
  4A:292-356
C:292-356
A:357-432
C:357-432
2TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.C1R_HUMAN464-702
 
  2B:447-685
D:447-685
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.C1R_HUMAN648-659
 
  2B:631-642
D:631-642

(-) Exons   (0, 0)

(no "Exon" information available for 2QY0)

(-) 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:154
 aligned with C1R_HUMAN | P00736 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:157
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       
            C1R_HUMAN   307 IKCPQPKTLDEFTIIQNLQPQYQFRDYFIATCKQGYQLIEGNQVLHSFTAVCQDDGTWHRAMPRCKIKDCGQPRNLPNGDFRYTTTMGVNTYKARIQYYCHEPYYKMQTRAGSRESEQGVYTCTAQGIWKNEQKGEKIPRCLPVCGKPVNPVEQRQR 463
               SCOP domains d2qy0a1 A:290-357 automated matches                                 d2qy0a2 A:358-446 automated matches                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee..........eeeeee...eeeee..eee...eee............eeee...........eeeee...........eeeeee....eee...---......eeee.....ee..........eee.............. Sec.struct. author
                 SAPs(SNPs) --W----------------------------R-------------------F-----C------W---------------------------------------------------------------R---------------------------- SAPs(SNPs)
                PROSITE (1) SUSHI  PDB: A:292-356 UniProt: 307-373                             SUSHI  PDB: A:357-432 UniProt: 374-449                                      -------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qy0 A 290 QACPQPKTLDEFTIIQNLQPQYQFRDYFIATCKQGYQLIEGNQVLHSFTAVCQDDGTWHRAMPRCKIKDCGQPRNLPNGDFRYTTTMGVNTYKARIQYYCHEPYYKMQTR---RESEQGVYTCTAQGIWKNEQKGEKIPRCLPVCGKPVNPVEQRQR 446
                                   299       309       319       329       339       349       359       369       379       389       399   |   409       419       429       439       
                                                                                                                                       399 403                                           

Chain B from PDB  Type:PROTEIN  Length:236
 aligned with C1R_HUMAN | P00736 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:240
                                   473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703
            C1R_HUMAN   464 IIGGQKAKMGNFPWQVFTNIHGRGGGALLGDRWILTAAHTLYPKEHEAQSNASLDVFLGHTNVEELMKLGNHPIRRVSVHPDYRQDESYNFEGDIALLELENSVTLGPNLLPICLPDNDTFYDLGLMGYVSGFGVMEEKIAHDLRFVRLPVANPQACENWLRGKNRMDVFSQNMFCAGHPSLKQDACQGDSGGVFAVRDPNTDRWVATGIVSWGIGCSRGYGFYTKVLNYVDWIKKEMEE 703
               SCOP domains d2qy0b_ B: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains 2qy0B01     2qy0B02 B:459-558,B:675-686 Trypsin    -like serine proteases                                       2qy0B01 B:447-458,B:559-674 Trypsin-like serine proteases                                                           2qy0B02      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeee...eeeehhhhhh.....----...eeee...hhhhhhhhh...eeeeee................eeeee.................hhhhhh...eeeeee............eeeeee..hhhhhhhhhhhh.........eeee................eeeee......eeeeeeeee........eeeee...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:447-685 UniProt: 464-702                                                                                                                                                                                                   - PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qy0 B 447 IIGGQKAKMGNFPWQVFTNIHGRGGGALLGDRWILTAAHTLYPKEHE----ASLDVFLGHTNVEELMKLGNHPIRRVSVHPDYRQDESYNFEGDIALLELENSVTLGPNLLPICLPDNDTFYDLGLMGYVSGFGVMEEKIAHDLRFVRLPVANPQACENWLRGKNRMDVFSQNMFCAGHPSLKQDACQGDSGGVFAVRDPNTDRWVATGIVSWGIGCSRGYGFYTKVLNYVDWIKKEMEE 686
                                   456       466       476       486      |  - |     506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686
                                                                        493  498                                                                                                                                                                                            

Chain C from PDB  Type:PROTEIN  Length:153
 aligned with C1R_HUMAN | P00736 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:157
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       
            C1R_HUMAN   307 IKCPQPKTLDEFTIIQNLQPQYQFRDYFIATCKQGYQLIEGNQVLHSFTAVCQDDGTWHRAMPRCKIKDCGQPRNLPNGDFRYTTTMGVNTYKARIQYYCHEPYYKMQTRAGSRESEQGVYTCTAQGIWKNEQKGEKIPRCLPVCGKPVNPVEQRQR 463
               SCOP domains d2qy0c1 C:290-357 automated matches                                 d2qy0c2 C:358-446 automated matches                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------Sushi-2qy0C01 C:359-430                                                 ---------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------Sushi-2qy0C02 C:359-430                                                 ---------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------Sushi-2qy0C03 C:359-430                                                 ---------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------Sushi-2qy0C04 C:359-430                                                 ---------------- Pfam domains (4)
         Sec.struct. author .ee.........eee......ee...eeeeee...eeeee..eee...eee............eeee...........eeeee...........eeeeee....eee...----.....eeee.....ee..........eee.............. Sec.struct. author
                 SAPs(SNPs) --W----------------------------R-------------------F-----C------W---------------------------------------------------------------R---------------------------- SAPs(SNPs)
                PROSITE (1) SUSHI  PDB: C:292-356 UniProt: 307-373                             SUSHI  PDB: C:357-432 UniProt: 374-449                                      -------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qy0 C 290 QACPQPKTLDEFTIIQNLQPQYQFRDYFIATCKQGYQLIEGNQVLHSFTAVCQDDGTWHRAMPRCKIKDCGQPRNLPNGDFRYTTTMGVNTYKARIQYYCHEPYYKMQTR----ESEQGVYTCTAQGIWKNEQKGEKIPRCLPVCGKPVNPVEQRQR 446
                                   299       309       319       329       339       349       359       369       379       389       399    |  409       419       429       439       
                                                                                                                                       399  404                                          

Chain D from PDB  Type:PROTEIN  Length:237
 aligned with C1R_HUMAN | P00736 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:240
                                   473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703
            C1R_HUMAN   464 IIGGQKAKMGNFPWQVFTNIHGRGGGALLGDRWILTAAHTLYPKEHEAQSNASLDVFLGHTNVEELMKLGNHPIRRVSVHPDYRQDESYNFEGDIALLELENSVTLGPNLLPICLPDNDTFYDLGLMGYVSGFGVMEEKIAHDLRFVRLPVANPQACENWLRGKNRMDVFSQNMFCAGHPSLKQDACQGDSGGVFAVRDPNTDRWVATGIVSWGIGCSRGYGFYTKVLNYVDWIKKEMEE 703
               SCOP domains d2qy0d_ D: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains 2qy0D01     2qy0D02 D:459-558,D:675-686 Trypsi   n-like serine proteases                                        2qy0D01 D:447-458,D:559-674 Trypsin-like serine proteases                                                           2qy0D02      CATH domains
           Pfam domains (1) Trypsin-2qy0D01 D:447-680                                                                                                                                                                                                                 ------ Pfam domains (1)
           Pfam domains (2) Trypsin-2qy0D02 D:447-680                                                                                                                                                                                                                 ------ Pfam domains (2)
         Sec.struct. author ....ee........eeeee...eeeeeee...eeeehhhhh.....---......eee...hhhhhhhhh...eeeeee................eeeee.................hhhhhh...eeeeee............eeeeee..hhhhhhhhhhhh.........eeee................eeeee......eeeeeeeee........eeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: D:447-685 UniProt: 464-702                                                                                                                                                                                                   - PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qy0 D 447 IIGGQKAKMGNFPWQVFTNIHGRGGGALLGDRWILTAAHTLYPKEH---SNASLDVFLGHTNVEELMKLGNHPIRRVSVHPDYRQDESYNFEGDIALLELENSVTLGPNLLPICLPDNDTFYDLGLMGYVSGFGVMEEKIAHDLRFVRLPVANPQACENWLRGKNRMDVFSQNMFCAGHPSLKQDACQGDSGGVFAVRDPNTDRWVATGIVSWGIGCSRGYGFYTKVLNYVDWIKKEMEE 686
                                   456       466       476       486     | 496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686
                                                                       492 496                                                                                                                                                                                              

   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/Biological Unit

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
1a2qy0B01B:447-458,B:559-674
1b2qy0D01D:447-458,D:559-674
1c2qy0D02D:459-558,D:675-686
1d2qy0B02B:459-558,B:675-686

(-) Pfam Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Family: Sushi (50)
2aSushi-2qy0C01C:359-430
2bSushi-2qy0C02C:359-430
2cSushi-2qy0C03C:359-430
2dSushi-2qy0C04C:359-430

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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 1gpz 1md7 1md8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2QY0)