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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X
 
Authors :  H. Mizuno, Z. Fujimoto, H. Atoda, T. Morita
Date :  27 Feb 01  (Deposition) - 27 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,G
Biol. Unit 1:  A,B,G  (1x)
Biol. Unit 2:  A,B,G  (2x)
Biol. Unit 3:  A,B,G  (2x)
Keywords :  Calcium Bridging, Domain Swapping, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mizuno, Z. Fujimoto, H. Atoda, T. Morita
Crystal Structure Of An Anticoagulant Protein In Complex With The Gla Domain Of Factor X.
Proc. Natl. Acad. Sci. Usa V. 98 7230 2001
PubMed-ID: 11404471  |  Reference-DOI: 10.1073/PNAS.131179698
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAGULATION FACTOR X BINDING PROTEIN
    Chains: A
    Organism Common: CHINESE MOCCASIN
    Organism Scientific: DEINAGKISTRODON ACUTUS
    Organism Taxid: 36307
 
Molecule 2 - COAGULATION FACTOR X BINDING PROTEIN
    Chains: B
    Organism Common: CHINESE MOCCASIN
    Organism Scientific: DEINAGKISTRODON ACUTUS
    Organism Taxid: 36307
 
Molecule 3 - COAGULATION FACTOR X GLA DOMAIN
    Chains: G
    EC Number: 3.4.21.6
    Fragment: GLA DOMAIN(RESIDUES 41-84)
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABG
Biological Unit 1 (1x): ABG
Biological Unit 2 (2x): ABG
Biological Unit 3 (2x): ABG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 24)

Asymmetric Unit (2, 24)
No.NameCountTypeFull Name
1CA12Ligand/IonCALCIUM ION
2CGU12Mod. Amino AcidGAMMA-CARBOXY-GLUTAMIC ACID
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CGU12Mod. Amino AcidGAMMA-CARBOXY-GLUTAMIC ACID
Biological Unit 2 (1, 24)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CGU24Mod. Amino AcidGAMMA-CARBOXY-GLUTAMIC ACID
Biological Unit 3 (1, 24)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CGU24Mod. Amino AcidGAMMA-CARBOXY-GLUTAMIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:41 , GLU A:43 , GLU A:47 , GLU A:128 , HOH A:568BINDING SITE FOR RESIDUE CA A 501
02AC2SOFTWARESER B:241 , GLN B:243 , GLU B:247 , GLU B:320 , HOH B:529 , HOH B:554BINDING SITE FOR RESIDUE CA B 502
03AC3SOFTWAREGLU A:98 , HOH B:505 , CGU G:425 , CGU G:429BINDING SITE FOR RESIDUE CA G 503
04AC4SOFTWAREHOH G:47 , HOH G:62 , CGU G:407 , CGU G:426 , CGU G:429BINDING SITE FOR RESIDUE CA G 504
05AC5SOFTWAREHOH G:63 , HOH G:102 , HOH G:125 , CGU G:407 , CGU G:416 , CGU G:426 , CGU G:429 , CA G:506BINDING SITE FOR RESIDUE CA G 505
06AC6SOFTWAREALA G:401 , ASN G:402 , CGU G:406 , CGU G:407 , CGU G:416 , CGU G:426 , CA G:505BINDING SITE FOR RESIDUE CA G 506
07AC7SOFTWAREHOH G:123 , ALA G:401 , CGU G:406 , CGU G:416 , CGU G:420BINDING SITE FOR RESIDUE CA G 507
08AC8SOFTWAREHOH G:37 , HOH G:143 , HOH G:149 , HOH G:190 , CGU G:420BINDING SITE FOR RESIDUE CA G 508
09AC9SOFTWAREHOH G:204 , HOH G:218 , CGU G:414 , CGU G:419BINDING SITE FOR RESIDUE CA G 509
10BC1SOFTWARECGU G:435 , CGU G:439BINDING SITE FOR RESIDUE CA G 510
11BC2SOFTWARESER A:80 , GLU A:82 , HOH A:580BINDING SITE FOR RESIDUE CA A 511
12BC3SOFTWAREASP A:1 , HOH A:575BINDING SITE FOR RESIDUE CA A 512

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:2 -A:13
2A:30 -A:127
3A:79 -B:275
4A:102 -A:119
5B:202 -B:213
6B:230 -B:319
7B:296 -B:311
8G:417 -G:422

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 5)

Asymmetric Unit (3, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLAB_DEIAC32-143  1B:209-320
SLUA_DEIAC32-151  1A:9-128
2GLA_1PS00011 Vitamin K-dependent carboxylation domain.FA10_BOVIN56-81  1G:416-441
3C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLAB_DEIAC119-142  1B:296-319
SLUA_DEIAC125-150  1A:102-127
Biological Unit 1 (3, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLAB_DEIAC32-143  1B:209-320
SLUA_DEIAC32-151  1A:9-128
2GLA_1PS00011 Vitamin K-dependent carboxylation domain.FA10_BOVIN56-81  1G:416-441
3C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLAB_DEIAC119-142  1B:296-319
SLUA_DEIAC125-150  1A:102-127
Biological Unit 2 (3, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLAB_DEIAC32-143  2B:209-320
SLUA_DEIAC32-151  2A:9-128
2GLA_1PS00011 Vitamin K-dependent carboxylation domain.FA10_BOVIN56-81  2G:416-441
3C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLAB_DEIAC119-142  2B:296-319
SLUA_DEIAC125-150  2A:102-127
Biological Unit 3 (3, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLAB_DEIAC32-143  2B:209-320
SLUA_DEIAC32-151  2A:9-128
2GLA_1PS00011 Vitamin K-dependent carboxylation domain.FA10_BOVIN56-81  2G:416-441
3C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLAB_DEIAC119-142  2B:296-319
SLUA_DEIAC125-150  2A:102-127

(-) Exons   (2, 2)

Asymmetric Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000217891ENSBTAE00000377900chr12:84664833-8466490270FA10_BOVIN1-24240--
1.2ENSBTAT000000217892ENSBTAE00000278163chr12:84666990-84667150161FA10_BOVIN24-77541G:401-43737
1.3ENSBTAT000000217893ENSBTAE00000177940chr12:84671119-8467114325FA10_BOVIN78-8691G:438-4447
1.4ENSBTAT000000217894ENSBTAE00000177941chr12:84672093-84672206114FA10_BOVIN86-124390--
1.5ENSBTAT000000217895ENSBTAE00000425962chr12:84673472-84673603132FA10_BOVIN124-168450--
1.6ENSBTAT000000217896ENSBTAE00000408790chr12:84675374-84675615242FA10_BOVIN168-248810--
1.7ENSBTAT000000217897ENSBTAE00000412504chr12:84676748-84676865118FA10_BOVIN249-288400--
1.8ENSBTAT000000217898ENSBTAE00000414972chr12:84677559-84678217659FA10_BOVIN288-4922050--

(-) 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:129
 aligned with SLUA_DEIAC | Q9IAM1 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:129
                                    33        43        53        63        73        83        93       103       113       123       133       143         
           SLUA_DEIAC    24 DCSSGWSSYEGHCYKVFKQSKTWTDAESFCTKQVNGGHLVSIESSGEADFVGQLIAQKIKSAKIHVWIGLRAQNKEKQCSIEWSDGSSISYENWIEEESKKCLGVHIETGFHKWENFYCEQQDPFVCEA 152
               SCOP domains d1ioda_ A: Snake coagglutinin alpha chain                                                                                         SCOP domains
               CATH domains 1iodA00 A:1-129 Mannose-Binding Protein A, subunit A                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhhhh...ee....hhhhhhhhhhhhhh........eeeeeee......................hhhhh..eeeehhhhh....eee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------C_TYPE_LECTIN_2  PDB: A:9-128 UniProt: 32-151                                                                           - PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -----------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           -- PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iod A   1 DCSSGWSSYEGHCYKVFKQSKTWADAESFCTKQVNGGHLVSIESSGEADFVGQLIAQKIKSAKIHVWIGLRAQNKEKQCSIEWSDGSSISYENWIEEESKKCLGVHIETGFHKWENFYCEQQDPFVCEA 129
                                    10        20        30        40        50        60        70        80        90       100       110       120         


Chain B from PDB  Type:PROTEIN  Length:123
 aligned with SLAB_DEIAC | Q9DEF8 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:123
                                    33        43        53        63        73        83        93       103       113       123       133       143   
           SLAB_DEIAC    24 DCPSDWSSYEGHCYKPFNEPKNWADAENFCTQQHTGSHLVSFQSTEEADFVVKLAFQTFDYGIFWMGLSKIWNQCNWQWSNAAMLKYTDWAEESYCVYFKSTNNKWRSITCRMIANFVCEFQA 146
               SCOP domains d1iodb_ B: Snake coagglutinin beta chain                                                                                    SCOP domains
               CATH domains 1iodB00 B:201-323 Mannose-Binding Protein A, subunit A                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhhhh...ee....hhhhhhhhhhhhhhhhh..eee...........eee...............eeeeee..eeeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: B:209-320 UniProt: 32-143                                                                 --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------C_TYPE_LECTIN_1         ---- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iod B 201 DCPSDWSSYEGHCYKPFNEPKNWADAENFCTQQHTGSHLVSFQSTEEADFVVKLAFQTFDYGIFWMGLSKIWNQCNWQWSNAAMLKYTDWAEESYCVYFKSTNNKWRSITCRMIANFVCEFQA 323
                                   210       220       230       240       250       260       270       280       290       300       310       320   


Chain G from PDB  Type:PROTEIN  Length:44
 aligned with FA10_BOVIN | P00743 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:44
                                    50        60        70        80    
           FA10_BOVIN    41 ANSFLEEVKQGNLERECLEEACSLEEAREVFEDAEQTDEFWSKY  84
               SCOP domains d1iodg_ G: Coagulation factor X              SCOP domains
               CATH domains 1iodG00 G:401-444 Coagulation Factor IX      CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author .......................................hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------GLA_1  PDB: G:416-441     --- PROSITE (3)
               Transcript 1 Exon 1.2  PDB: G:401-437 [INCOMPLETE]1.3     Transcript 1
                 1iod G 401 ANSFLeeVKQGNLeReCLeeACSLeeAReVFeDAeQTDeFWSKY 444
                                 ||410   | | 420    || 430 |  |  440    
                                 ||      | |  ||    ||  |  |  |   |     
                               406-CGU   | |  ||    ||  |  |  |   |     
                                407-CGU  | |  ||    ||  |  |  |   |     
                                       414-CGU||    ||  |  |  |   |     
                                         416-CGU    ||  |  |  |   |     
                                            419-CGU ||  |  |  |   |     
                                             420-CGU||  |  |  |   |     
                                                  425-CGU  |  |   |     
                                                   426-CGU |  |   |
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (2, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (SLUA_DEIAC | Q9IAM1)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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 B   (SLAB_DEIAC | Q9DEF8)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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 G   (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.

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  1iod
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 Related Entries

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

UniProtKB/Swiss-Prot
        FA10_BOVIN | P00743: 1apo 1ccf 1kig 1whe 1whf
        SLAB_DEIAC | Q9DEF8: 1wt9 1y17
        SLUA_DEIAC | Q9IAM1: 1wt9

(-) Related Entries Specified in the PDB File

1bj3 1BJ3 CONTAINS THE FACTOR IX BINDING PROTEIN
1ixx 1IXX CONTAINS THE FACTOR IX/FACTOR X BINDING PROTEIN