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(-) Description

Title :  CRYSTAL STRUCTURE OF COAGULATION FACTOR IX-BINDING PROTEIN (IX-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS
 
Authors :  H. Mizuno, Z. Fujimoto, M. Koizumi, H. Kano, H. Atoda, T. Morita
Date :  02 Jul 98  (Deposition) - 16 Aug 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Coagulation Factor Ix-Binding, Heterodimer, Venom, Habu Snake, C-Type Lectin Superfamily, Collagen Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mizuno, Z. Fujimoto, M. Koizumi, H. Kano, H. Atoda, T. Morita
Crystal Structure Of Coagulation Factor Ix-Binding Protein From Habu Snake Venom At 2. 6 A: Implication Of Central Loop Swapping Based On Deletion In The Linker Region.
J. Mol. Biol. V. 289 103 1999
PubMed-ID: 10339409  |  Reference-DOI: 10.1006/JMBI.1999.2756
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (COAGULATION FACTOR IX-BINDING PROTEIN A)
    Chains: A
    Fragment: C-TYPE LECTIN CRD DOMAIN
    Organism Scientific: TRIMERESURUS FLAVOVIRIDIS
    Organism Taxid: 88087
    Other Details: DISULPHIDE DIMER BETWEEN A CYS79 AND B CYS75, PROTEIN COMPOSED OF HOMOLOGOUS SUBUNITS TO THE CARBOHYDRATE RECOGNITION DOMAIN OF C-TYPE LECTIN
    Secretion: VENOM
    Synonym: IX-BP
 
Molecule 2 - PROTEIN (COAGULATION FACTOR IX-BINDING PROTEIN B)
    Chains: B
    Fragment: C-TYPE LECTIN CRD DOMAIN
    Organism Scientific: TRIMERESURUS FLAVOVIRIDIS
    Organism Taxid: 88087
    Other Details: DISULPHIDE DIMER BETWEEN A CYS79 AND B CYS75, PROTEIN COMPOSED OF HOMOLOGOUS SUBUNITS TO THE CARBOHYDRATE RECOGNITION DOMAIN OF C-TYPE LECTIN
    Secretion: VENOM
    Synonym: IX-BP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:41 , GLU A:43 , GLU A:47 , GLU A:128 , HOH A:170 , HOH A:171BINDING SITE FOR RESIDUE CA A 130
2AC2SOFTWARESER B:41 , GLN B:43 , GLU B:47 , GLU B:120 , HOH B:157 , HOH B:162BINDING SITE FOR RESIDUE CA B 124

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:2 -A:13
2A:30 -A:127
3A:79 -B:75
4A:102 -A:119
5B:2 -B:13
6B:30 -B:119
7B:96 -B:111

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BJ3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BJ3)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLA_PROFL9-128  1A:9-128
SL9B_PROFL32-143  1B:9-120
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLA_PROFL102-127  1A:102-127
SL9B_PROFL119-142  1B:96-119

(-) Exons   (0, 0)

(no "Exon" information available for 1BJ3)

(-) 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:129
 aligned with SLA_PROFL | Q7LZ71 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
            SLA_PROFL     1 DCPSGWSSYEGHCYKPFKLYKTWDDAERFCTEQAKGGHLVSIESAGEADFVAQLVTENIQNTKSYVWIGLRVQGKEKQCSSEWSDGSSVSYENWIEAESKTCLGLEKETGFRKWVNIYCGQQNPFVCEA 129
               SCOP domains d1bj3a_ A: Snake coagglutinin alpha chain                                                                                         SCOP domains
               CATH domains 1bj3A00 A:1-129 Mannose-Binding Protein A, subunit A                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeee...hhhhhhhhhhh...........hhhhhhhhhhhh.........eeeeee..............................eeee........eeeee....eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: A:9-128 UniProt: 9-128                                                                            - PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           -- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bj3 A   1 DCPSGWSSYEGHCYKPFKLYKTWDDAERFCTEQAKGGHLVSIESAGEADFVAQLVTENIQNTKSYVWIGLRVQGKEKQCSSEWSDGSSVSYENWIEAESKTCLGLEKETGFRKWVNIYCGQQNPFVCEA 129
                                    10        20        30        40        50        60        70        80        90       100       110       120         


Chain B from PDB  Type:PROTEIN  Length:123
 aligned with SL9B_PROFL | P23807 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:123
                                    33        43        53        63        73        83        93       103       113       123       133       143   
           SL9B_PROFL    24 DCPSDWSSYEGHCYKPFSEPKNWADAENFCTQQHAGGHLVSFQSSEEADFVVKLAFQTFGHSIFWMGLSNVWNQCNWQWSNAAMLRYKAWAEESYCVYFKSTNNKWRSRACRMMAQFVCEFQA 146
               SCOP domains d1bj3b_ B: Snake coagglutinin beta chain                                                                                    SCOP domains
               CATH domains 1bj3B00 B:1-123 Mannose-Binding Protein A, subunit A                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeee...hhhhhhhhhhh...........hhhhhhhhhhhh.......eeeeee..........................eeee......eeeee....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------C_TYPE_LECTIN_2  PDB: B:9-120 UniProt: 32-143                                                                   --- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -----------------------------------------------------------------------------------------------C_TYPE_LECTIN_1         ---- PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bj3 B   1 DCPSDWSSYEGHCYKPFSEPKNWADAENFCTQQHAGGHLVSFQSSEEADFVVKLAFQTFGHSIFWMGLSNVWNQCNWQWSNAAMLRYKAWAEESYCVYFKSTNNKWRSRACRMMAQFVCEFQA 123
                                    10        20        30        40        50        60        70        80        90       100       110       120
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BJ3)

(-) Gene Ontology  (3, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SLA_PROFL | Q7LZ71)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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   (SL9B_PROFL | P23807)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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.

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  1bj3
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 Related Entries

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

UniProtKB/Swiss-Prot
        SL9B_PROFL | P23807: 1ixx 1j34 1j35 1x2t 1x2w
        SLA_PROFL | Q7LZ71: 1j34 1j35 1x2t 1x2w

(-) Related Entries Specified in the PDB File

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