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(-) Description

Title :  CRYSTAL STRUCTURE OF COBRA VENOM FACTOR, A CO-FACTOR FOR C3-AND C5 CONVERTASE CVFBB
 
Authors :  V. Krishnan, S. V. L. Narayana
Date :  08 Jan 09  (Deposition) - 28 Apr 09  (Release) - 28 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym./Biol. Unit :  A,B,G
Keywords :  Cobra Venom Factor, Naja Naja Kouthia, Complement C3 And C5 Convertase Cvfbb, Complement Proteins, Complement Alternate Pathway, Complement Pathway, Glycoprotein, Immune Response, Inflammatory Response, Innate Immunity, Secreted, Thioester Bond, Toxin, Hydrolase Cofactor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Krishnan, K. Ponnuraj, Y. Xu, K. Macon, J. E. Volanakis, S. V. Narayana
The Crystal Structure Of Cobra Venom Factor, A Cofactor For C3- And C5-Convertase Cvfbb.
Structure V. 17 611 2009
PubMed-ID: 19368894  |  Reference-DOI: 10.1016/J.STR.2009.01.015
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COBRA VENOM FACTOR ALPHA CHAIN
    Chains: A
    Organism Common: MONOCLED COBRA
    Organism Scientific: NAJA KAOUTHIA
    Organism Taxid: 8649
    Secretion: VENOM
    Synonym: CVF, COMPLEMENT C3 HOMOLOG, COBRA VENOM FACTOR ALPHA CHAIN, COBRA VENOM FACTOR GAMMA CHAIN, COBRA VENOM FACTOR BETA CHAIN
 
Molecule 2 - COBRA VENOM FACTOR GAMMA CHAIN
    Chains: G
    Organism Common: MONOCLED COBRA
    Organism Scientific: NAJA KAOUTHIA
    Organism Taxid: 8649
    Secretion: VENOM
    Synonym: CVF, COMPLEMENT C3 HOMOLOG, COBRA VENOM FACTOR ALPHA CHAIN, COBRA VENOM FACTOR GAMMA CHAIN, COBRA VENOM FACTOR BETA CHAIN
 
Molecule 3 - COBRA VENOM FACTOR BETA CHAIN
    Chains: B
    Organism Common: MONOCLED COBRA
    Organism Scientific: NAJA KAOUTHIA
    Organism Taxid: 8649
    Secretion: VENOM
    Synonym: CVF, COMPLEMENT C3 HOMOLOG, COBRA VENOM FACTOR ALPHA CHAIN, COBRA VENOM FACTOR GAMMA CHAIN, COBRA VENOM FACTOR BETA CHAIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABG

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:494 , ASP A:517 , VAL A:518 , ASP A:520 , HOH A:641BINDING SITE FOR RESIDUE CA A 628

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1A:522 -G:779
2A:587 -A:622
3B:1318 -B:1446
4B:1346 -B:1415
5B:1463 -B:1468
6B:1475 -B:1547
7B:1494 -B:1618
8B:1594 -B:1603
9G:835 -B:1470

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:39 -Pro A:40
2Ile A:493 -Pro A:494
3His B:1480 -Gln B:1481

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NTRPS50189 NTR domain profile.VCO3_NAJKA1497-1640  1B:1475-1618

(-) Exons   (0, 0)

(no "Exon" information available for 3FRP)

(-) 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:602
 aligned with VCO3_NAJKA | Q91132 from UniProtKB/Swiss-Prot  Length:1642

    Alignment length:623
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642   
          VCO3_NAJKA     23 ALYTLITPAVLRTDTEEQILVEAHGDSTPKQLDIFVHDFPRKQKTLFQTRVDMNPAGGMLVTPTIEIPAKEVSTDSRQNQYVVVQVTGPQVRLEKVVLLSYQSSFLFIQTDKGIYTPGSPVLYRVFSMDHNTSKMNKTVIVEFQTPEGILVSSNSVDLNFFWPYNLPDLVSLGTWRIVAKYEHSPENYTAYFDVRKYVLPSFEVRLQPSEKFFYIDGNENFHVSITARYLYGEEVEGVAFVLFGVKIDDAKKSIPDSLTRIPIIDGDGKATLKRDTFRSRFPNLNELVGHTLYASVTVMTESGSDMVVTEQSGIHIVASPYQIHFTKTPKYFKPGMPYELTVYVTNPDGSPAAHVPVVSEAFHSMGTTLSDGTAKLILNIPLNAQSLPITVRTNHGDLPRERQATKSMTAIAYQTQGGSGNYLHVAITSTEIKPGDNLPVNFNVKGNANSLKQIKYFTYLILNKGKIFKVGRQPRRDGQNLVTMNLHITPDLIPSFRFVAYYQVGNNEIVADSVWVDVKDTCMGTLVVKGDNLIQMPGAAMKIKLEGDPGARVGLVAVDKAVYVLNDKYKISQAKIWDTIEKSDFGCTAGSGQNNLGVFEDAGLALTTSTNLNTKQRSAAKCP  645
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.eee....ee.eeeee.....eeeeeeeeee.....eeeeeeeeehhhhh.ee..ee.....--------..eeeeeeee..eeeeeeeeee.....eeeee...ee....ee.eeeee.---------.eeeeee.....eee..ee.......ee.......eeeeeeeee......eeeeeee.......eeeeeee...eee......eeeeeeeee.......eeeeeeeeeee..eeee.....eeeee...eeeeeehhhhhhhhh.----....eeeeeeeeee.....eeeeeeeeeeee....eee......ee.....eeeeeeee..........eeeehhhheeee.....eeeeee.......eeeeeeee.....hhhhh.eeeeeeee.........eeeee..........eeeeeeeee.hhhhhh...eeeeeeee..eeeeeeeee......eeeeeee.hhhhh.eeeeeeeeee...eeeeeeeeee.........eee..........eeeeeeee....eeeeeeeehhhhhhh.....hhhhhhhhhhh...........hhhhhhhhh.eeeee............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3frp A    1 ALYTLITPAVLRTDTEEQILVEAHGDSTPKQLDIFVHDFPRKQKTLFQTRVDMNPAGGMLVTPTIEIPAK--------NQYVVVQVTGPQVRLEKVVLLSYQSSFLFIQTDKGIYTPGSPVLYRVFSM---------TVIVEFQTPEGILVSSNSVDLNFFWPYNLPDLVSLGTWRIVAKYEHSPENYTAYFDVRKYVLPSFEVRLQPSEKFFYIDGNENFHVSITARYLYGEEVEGVAFVLFGVKIDDAKKSIPDSLTRIPIIDGDGKATLKRDTFRSRFP----LVGHTLYASVTVMTESGSDMVVTEQSGIHIVASPYQIHFTKTPKYFKPGMPYELTVYVTNPDGSPAAHVPVVSEAFHSMGTTLSDGTAKLILNIPLNAQSLPITVRTNHGDLPRERQATKSMTAIAYQTQGGSGNYLHVAITSTEIKPGDNLPVNFNVKGNANSLKQIKYFTYLILNKGKIFKVGRQPRRDGQNLVTMNLHITPDLIPSFRFVAYYQVGNNEIVADSVWVDVKDTCMGTLVVKGDNLIQMPGAAMKIKLEGDPGARVGLVAVDKAVYVLNDKYKISQAKIWDTIEKSDFGCTAGSGQNNLGVFEDAGLALTTSTNLNTKQRSAAKCP  623
                                    10        20        30        40        50        60        70        80        90       100       110       120       | -       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280 |    |290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620   
                                                                                                70       79                                              128       138                                                                                                                                             282  287                                                                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:343
 aligned with VCO3_NAJKA | Q91132 from UniProtKB/Swiss-Prot  Length:1642

    Alignment length:368
                                  1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382      1392      1402      1412      1422      1432      1442      1452      1462      1472      1482      1492      1502      1512      1522      1532      1542      1552      1562      1572      1582      1592      1602      1612      1622      1632        
          VCO3_NAJKA   1273 LNLDITIELPDREVPIRYRINYENALLARTVETKLNQDITVTASGDGKATMTILTFYNAQLQEKANVCNKFHLNVSVENIHLNAMGAKGALMLKICTRYLGEVDSTMTIIDISMLTGFLPDAEDLTRLSKGVDRYISRYEVDNNMAQKVAVIIYLNKVSHSEDECLHFKILKHFEVGFIQPGSVKVYSYYNLDEKCTKFYHPDKGTGLLNKICIGNVCRCAGETCSSLNHQERIDVPLQIEKACETNVDYVYKTKLLRIEEQDGNDIYVMDVLEVIKQGTDENPRAKTHQYISQRKCQEALNLKVNDDYLIWGSRSDLLPTKDKISYIITKNTWIERWPHEDECQEEEFQKLCDDFAQFSYTLTEFGC 1640
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.......eee...-------...ee.....eeee..----.eeeeeeeeee.------....eeeeeeeee..--------.eeeeeeeee.....eeeeeeeee....eeehhhhhhhhhh..........ee..ee...eeeeeeeee.....eeeeeeeee.........eeeeeee..eeeeeeeeee..........eeee..eeee..............hhhhhhhhh......eeeeeeeeeee......eeeeeeeeeee...........eeee.hhhhh.........eeeeee...........eeee.....eeeee..........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NTR  PDB: B:1475-1618 UniProt: 1497-1640                                                                                                         PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3frp B 1251 LNLDITIELPDREVPIRYRIN-------RTVETKLNQDITVTAS----ATMTILTFYNAQ------VCNKFHLNVSVENIH--------ALMLKICTRYLGEVDSTMTIIDISMLTGFLPDAEDLTRLSKGVDRYISRYEVDNNMAQKVAVIIYLNKVSHSEDECLHFKILKHFEVGFIQPGSVKVYSYYNLDEKCTKFYHPDKGTGLLNKICIGNVCRCAGETCSSLNHQERIDVPLQIEKACETNVDYVYKTKLLRIEEQDGNDIYVMDVLEVIKQGTDENPRAKTHQYISQRKCQEALNLKVNDDYLIWGSRSDLLPTKDKISYIITKNTWIERWPHEDECQEEEFQKLCDDFAQFSYTLTEFGC 1618
                                  1260      1270|     1280      1290   |  1300      1310      1320      1330|     1340      1350      1360      1370      1380      1390      1400      1410      1420      1430      1440      1450      1460      1470      1480      1490      1500      1510      1520      1530      1540      1550      1560      1570      1580      1590      1600      1610        
                                             1271    1279           1294 1299       1310   1317          1331     1340                                                                                                                                                                                                                                                                                      


Chain G from PDB  Type:PROTEIN  Length:215
 aligned with VCO3_NAJKA | Q91132 from UniProtKB/Swiss-Prot  Length:1642

    Alignment length:230
                                   748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968
          VCO3_NAJKA    739 FIADSDIISRSDFPKSWLWLTKDLTEEPNSQGISSKTMSFYLRDSITTWVVLAVSFTPTKGICVAEPYEIRVMKVFFIDLQMPYSVVKNEQVEIRAILHNYVNEDIYVRVELLYNPAFCSASTKGQRYRQQFPIKALSSRAVPFVIVPLEQGLHDVEIKASVQEALWSDGVRKKLKVVPEGVQKSIVTIVKLDPRAKGVGGTQLEVIKARKLDDRVPDTEIETKIIIQGD  968
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeee..........eeeeeeee.....eeeeeeeeeee...eeee...eeeee...eeeee.....ee....eeeeeeeee.....eeeeeee.....ee........eeeeeee...eeeeeeeeeee...eeeeeeeeeee.....eeeeeeeeeee...eeeeeeeeeee..-------..eeee...--------...eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3frp G  717 FIADSDIISRSDFPKSWLWLTKDLTEEPNSQGISSKTMSFYLRDSITTWVVLAVSFTPTKGICVAEPYEIRVMKVFFIDLQMPYSVVKNEQVEIRAILHNYVNEDIYVRVELLYNPAFCSASTKGQRYRQQFPIKALSSRAVPFVIVPLEQGLHDVEIKASVQEALWSDGVRKKLKVVPEGVQKSIVTIVKLDP-------TQLEVIKAR--------TEIETKIIIQGD  946
                                   726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906   |     - |     926       936       946
                                                                                                                                                                                                                           910     918     926      935
   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 3FRP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FRP)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,G   (VCO3_NAJKA | Q91132)
molecular function
    GO:0004866    endopeptidase inhibitor activity    Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
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:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
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.
    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
        VCO3_NAJKA | Q91132: 3hrz 3hs0 3prx 3pvm

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3FRP)