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(-) Description

Title :  BOVINE FACTOR XA
 
Authors :  A. Wei, R. Alexander, C. -H. Chang
Date :  24 Apr 97  (Deposition) - 28 Oct 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  H,I,L
Keywords :  Glycoprotein, Serine Protease, Plasma, Blood Coagulation, Complex (Protease/Inhibitor) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Wei, R. S. Alexander, J. Duke, H. Ross, S. A. Rosenfeld, C. H. Chang
Unexpected Binding Mode Of Tick Anticoagulant Peptide Complexed To Bovine Factor Xa.
J. Mol. Biol. V. 283 147 1998
PubMed-ID: 9761680  |  Reference-DOI: 10.1006/JMBI.1998.2069
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FACTOR XA
    ChainsH
    EC Number3.4.21.6
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System Taxid4932
    OrganBLOOD
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
 
Molecule 2 - FACTOR XA
    ChainsL
    EC Number3.4.21.6
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System Taxid4932
    OrganBLOOD
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
 
Molecule 3 - ANTICOAGULANT PEPTIDE
    ChainsI
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System Taxid4932
    OrganBLOOD
    Organism ScientificORNITHODOROS MOUBATA
    Organism Taxid6938
    SynonymRTAP

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit HIL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1KIG)

(-) Sites  (0, 0)

(no "Site" information available for 1KIG)

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:27
2H:42 -H:58
3H:122 -L:432
4H:168 -H:182
5H:191 -H:220
6I:505 -I:559
7I:515 -I:539
8I:533 -I:555
9L:389 -L:400
10L:396 -L:409
11L:411 -L:424

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KIG)

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_2PS01186 EGF-like domain signature 2.FA10_BOVIN110-121
149-164
  1-
L:409-424
2TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.FA10_BOVIN234-466  1H:16-243
3TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.FA10_BOVIN271-276  1H:53-58
4TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.FA10_BOVIN412-423  1H:189-200

(-) Exons   (4, 5)

Asymmetric/Biological Unit (4, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000217891ENSBTAE00000377900chr12:84664833-8466490270FA10_BOVIN1-24240--
1.2ENSBTAT000000217892ENSBTAE00000278163chr12:84666990-84667150161FA10_BOVIN24-77540--
1.3ENSBTAT000000217893ENSBTAE00000177940chr12:84671119-8467114325FA10_BOVIN78-8690--
1.4ENSBTAT000000217894ENSBTAE00000177941chr12:84672093-84672206114FA10_BOVIN86-124390--
1.5ENSBTAT000000217895ENSBTAE00000425962chr12:84673472-84673603132FA10_BOVIN124-168451-
L:389-428
-
40
1.6ENSBTAT000000217896ENSBTAE00000408790chr12:84675374-84675615242FA10_BOVIN168-248812H:16-30
L:428-439
15
12
1.7ENSBTAT000000217897ENSBTAE00000412504chr12:84676748-84676865118FA10_BOVIN249-288401H:31-69
-
40
-
1.8ENSBTAT000000217898ENSBTAE00000414972chr12:84677559-84678217659FA10_BOVIN288-4922051H:69-251 (gaps)
-
189
-

(-) 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 H from PDB  Type:PROTEIN  Length:241
 aligned with FA10_BOVIN | P00743 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:241
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473 
          FA10_BOVIN    234 IVGGRDCAEGECPWQALLVNEENEGFCGGTILNEFYVLTAAHCLHQAKRFTVRVGDRNTEQEEGNEMAHEVEMTVKHSRFVKETYDFDIAVLRLKTPIRFRRNVAPACLPEKDWAEATLMTQKTGIVSGFGRTHEKGRLSSTLKMLEVPYVDRSTCKLSSSFTITPNMFCAGYDTQPEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKFGVYTKVSNFLKWIDKIMKARAGAAGS  474
               SCOP domains d1kigh_ H: Coagulation factor Xa, protease domain                                                                                                                                                                                                 SCOP domains
               CATH domains 1kigH01     1kigH02 H:28-120,H:233-246 Trypsin-like serine proteases                                      1kigH01 H:16-27,H:121-232 Trypsin-like serine proteases                                                             1kigH02       ----- CATH domains
               Pfam domains Trypsin-1kigH01 H:16-238                                                                                                                                                                                                            ------------- Pfam domains
         Sec.struct. author ..............eeeee.....eeeeee.....eeee...............................eeeeee.............eeeee.................hhhhhh......eeeeee..............eeeeee...hhhhhhh........eeee................eeeeee..eeeeeeeeee..........eeeeehhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: H:16-243 UniProt: 234-466                                                                                                                                                                                              -------- PROSITE (1)
                PROSITE (2) -------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------------- PROSITE (2)
           Transcript 1 (1) ---------------Exon 1.7  PDB: H:31-69 UniProt: 249-288 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) Exon 1.6       ---------------------------------------Exon 1.8  PDB: H:69-251 (gaps) UniProt: 288-492 [INCOMPLETE]                                                                                                                                Transcript 1 (2)
                1kig H   16 IVGGRDCAEGECPWQALLVNEENEGFCGGTILNEFYVLTAAHCLHQAKRFTVRVGDRNTEQEEGNEMAHEVEMTVKHSRFVKETYDFDIAVLRLKTPIRFRRNVAPACLPEKDWAEATLMTQKTGIVSGFGRTHEKGRLSSTLKMLEVPYVDRSTCKLSSSFTITPNMFCAGYDTQPEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKFGVYTKVSNFLKWIDKIMKARAGAAGS  251
                                    25        35        45        55      | 64        74        84        94       104       114       124|     131B       141       152       162       172       182   ||  190       200       210       221  |    230       240       250 
                                                                        61A                                                            124A    131A|                150|                              185A|                              218|   |                            
                                                                                                                                                131B                 152                               185B                               220   |                            
                                                                                                                                                                                                                                             223A                            

Chain I from PDB  Type:PROTEIN  Length:60
 aligned with TAP_ORNMO | P17726 from UniProtKB/Swiss-Prot  Length:60

    Alignment length:60
                                    10        20        30        40        50        60
           TAP_ORNMO      1 YNRLCIKPRDWIDECDSNEGGERAYFRNGKGGCDSFWICPEDHTGADYYSSYRDCFNACI   60
               SCOP domains d1kigi_ I: Anticoagulant protein, factor Xa inhibitor        SCOP domains
               CATH domains 1kigI00 I:501-560 Factor Xa Inhibitor                        CATH domains
               Pfam domains ---Kunitz_BPTI-1kigI01 I:504-560                             Pfam domains
         Sec.struct. author ..hhh................eee...........eee...................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                1kig I  501 YNRLCIKPRDWIDECDSNEGGERAYFRNGKGGCDSFWICPEDHTGADYYSSYRDCFNACI  560
                                   510       520       530       540       550       560

Chain L from PDB  Type:PROTEIN  Length:51
 aligned with FA10_BOVIN | P00743 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:51
                                   138       148       158       168       178 
          FA10_BOVIN    129 CSLDNGGCDQFCREERSEVRCSCAHGYVLGDDSKSCVSTERFPCGKFTQGR  179
               SCOP domains d1kigl_ L: Factor X, N-terminal module              SCOP domains
               CATH domains 1kigL00 L:389-439 Laminin                           CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ..........................eee......eee............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------EGF_2           --------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.5  PDB: L:389-428 [INCOMPLETE]   ----------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.6     Transcript 1 (2)
                1kig L  389 CSLDNGGCDQFCREERSEVRCSCAHGYVLGDDSKSCVSTERFPCGKFTQGR  439
                                   398       408       418       428       438 

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 4)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H,L   (FA10_BOVIN | P00743)
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:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    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:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0051897    positive regulation of protein kinase B signaling    Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    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 I   (TAP_ORNMO | P17726)
molecular function
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    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.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FA10_BOVIN | P007431apo 1ccf 1iod 1whe 1whf
        TAP_ORNMO | P177261d0d 1tap 1tcp

(-) Related Entries Specified in the PDB File

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