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(-) Description

Authors :  H. Jing, Y. S. Babu, D. Moore, J. M. Kilpatrick, X. -Y. Liu, J. E. Volanaki S. V. L. Narayana
Date :  18 Jun 98  (Deposition) - 22 Jun 99  (Release) - 13 Jul 11  (Revision)
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine Protease, Hydrolase, Complement, Factor D, Catalytic Triad, Self-Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  H. Jing, Y. S. Babu, D. Moore, J. M. Kilpatrick, X. Y. Liu, J. E. Volanakis, S. V. Narayana
Structures Of Native And Complexed Complement Factor D: Implications Of The Atypical His57 Conformation And Self-Inhibitory Loop In The Regulation Of Specific Serine Protease Activity.
J. Mol. Biol. V. 282 1061 1998
PubMed-ID: 9753554  |  Reference-DOI: 10.1006/JMBI.1998.2089
(for further references see the PDB file header)

(-) Compounds

    EC Number3.4.21.46
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
1AC1SOFTWARECYS A:191 , LYS A:192 , SER A:195 , THR A:214 , SER A:215 , ARG A:218 , HOH A:390BINDING SITE FOR RESIDUE SOA A 244
2AC2SOFTWAREASP A:129A , VAL A:130 , VAL A:162 , LEU A:163 , ASP A:164 , ARG A:165 , MET A:181 , CYS A:182 , HOH A:313BINDING SITE FOR RESIDUE GOL A 245

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
1A:42 -A:58
2A:136 -A:201
3A:168 -A:182
4A:191 -A:220

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BIO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034866V213GCFAD_HUMANDisease (CFDD)267606720AV200G
2UniProtVAR_034867C214RCFAD_HUMANDisease (CFDD)267606721AC201R

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CFAD_HUMAN26-253  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CFAD_HUMAN62-67  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CFAD_HUMAN202-213  1A:189-200

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003277262ENSE00001231561chr19:860617-860773157CFAD_HUMAN19-71531A:16-61A (gaps)47
1.4ENST000003277264ENSE00001374327chr19:861699-861956258CFAD_HUMAN120-205861A:108-192 (gaps)89
1.5ENST000003277265ENSE00001354943chr19:863092-863606515CFAD_HUMAN206-253481A:193-243 (gaps)52

(-) 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:228
 aligned with CFAD_HUMAN | P00746 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:228
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245        
               SCOP domains d1bioa_ A: Factor D                                                                                                                                                                                                                  SCOP domains
               CATH domains 1bioA01     1bioA02 A:28-122,A:233-243 Trypsin-like serine proteases                                       1bioA01 A:16-27,A:123-232 Trypsin-like serine proteases                                                       1bioA02     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeeee..eeeeeeeeee..eeee.hhhhhh.....eeeee............eeeeeeeeee.............eeeee..........................eeeeee..............eeeeee...hhhhh............eeee..............eeee..eeeeee.............eeeeehhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GR---------------------------------M----- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 26-253                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI--------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ---------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:16-61A (gaps) UniProt: 19-71 ------------------------------------------------Exon 1.4  PDB: A:108-192 (gaps) UniProt: 120-205                                      Exon 1.5  PDB: A:193-243 (gaps) UniProt: 206-253 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3  PDB: A:61A-107 UniProt: 71-119         -------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                                    25        35||      46        56     |||63        73        83        93       103       113 ||   124A     | 133       143   ||  154       164      |172       182       192       202|      216       225       235        
                                               36|                     61A||                                                   115|   124A  129A               147|                  170A|                             202|             223A                    
                                                38                      61B|                                                    118                             149                   170B                              207                                     

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CFAD_HUMAN | P00746)
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: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:0006957    complement activation, alternative pathway    Any process involved in the activation of any of the steps of the alternative pathway of the complement cascade which allows for the direct killing of microbes 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:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.
    GO:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.


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 Related Entries

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

        CFAD_HUMAN | P007461dfp 1dic 1dst 1dsu 1fdp 1hfd 2xw9 2xwa 2xwb 4cbn 4cbo 4d9r 5fbe 5fbi 5fck 5mt0 5mt4 5nar 5naw 5nb6 5nb7 5nba 5tca 5tcc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BIO)