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(-) Description

Title :  CRYSTAL STRUCTURE OF APO-HABU IX-BP AT PH 4.6
 
Authors :  N. Suzuki, Z. Fujimoto, T. Morita, A. Fukamizu, H. Mizuno
Date :  26 Apr 05  (Deposition) - 04 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Heterodimer, Domain Swapping, C-Type Lectin-Like Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Suzuki, Z. Fujimoto, T. Morita, A. Fukamizu, H. Mizuno
Ph-Dependent Structural Changes At Ca(2+)-Binding Sites Of Coagulation Factor Ix-Binding Protein
J. Mol. Biol. V. 353 80 2005
PubMed-ID: 16165155  |  Reference-DOI: 10.1016/J.JMB.2005.08.018
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAGULATION FACTOR IX/X-BINDING PROTEIN A CHAIN
    Chains: A
    Organism Scientific: TRIMERESURUS FLAVOVIRIDIS
    Organism Taxid: 88087
    Secretion: VENOM
 
Molecule 2 - COAGULATION FACTOR IX/FACTOR X-BINDING PROTEIN B CHAIN
    Chains: B
    Organism Scientific: TRIMERESURUS FLAVOVIRIDIS
    Organism Taxid: 88087
    Secretion: VENOM
    Synonym: IX/X-BP

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2RB2Ligand/IonRUBIDIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2RB-1Ligand/IonRUBIDIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2RB-1Ligand/IonRUBIDIUM ION
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:73 , GLY A:74 , GLU A:76 , TYR A:91 , ASN B:76BINDING SITE FOR RESIDUE CL A 401
2AC2SOFTWAREHOH A:564BINDING SITE FOR RESIDUE RB A 402
3AC3SOFTWARECYS A:2 , PRO A:3 , TRP A:6 , HOH A:437BINDING SITE FOR RESIDUE RB A 403
4AC4SOFTWAREASP A:24 , ARG A:71 , GLY A:74 , LYS A:75 , CYS A:119 , HOH A:456 , HOH A:479 , HOH A:489BINDING SITE FOR RESIDUE SO4 A 404

(-) SS Bonds  (7, 7)

Asymmetric 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 1X2W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X2W)

(-) PROSITE Motifs  (2, 4)

Asymmetric 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
Biological Unit 1 (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
Biological Unit 2 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLA_PROFL9-128  2A:9-128
SL9B_PROFL32-143  2B:9-120
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLA_PROFL102-127  2A:102-127
SL9B_PROFL119-142  2B:96-119

(-) Exons   (0, 0)

(no "Exon" information available for 1X2W)

(-) 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 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 d1x2wa_ A: Snake coagglutinin alpha chain                                                                                         SCOP domains
               CATH domains 1x2wA00 A:1-129 Mannose-Binding Protein A, subunit A                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhhhh...ee....hhhhhhhhhhhhhhhh......eeeeeee......................hhhhh..eeee.........eee.....eeeeee. 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
                 1x2w 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 d1x2wb_ B: Snake coagglutinin beta chain                                                                                    SCOP domains
               CATH domains 1x2wB00 B:1-123 Mannose-Binding Protein A, subunit A                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee...eeeeeeeeeehhhhhhhhhhh.....ee....hhhhhhhhhhhhhhhhh..eee...........eee...............eeeeee......eeee....eeeeeeee. 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
                 1x2w 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)
    → 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  (2, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1X2W)

(-) Gene Ontology  (3, 6)

Asymmetric 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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 Related Entries

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

UniProtKB/Swiss-Prot
        SL9B_PROFL | P23807: 1bj3 1ixx 1j34 1j35 1x2t
        SLA_PROFL | Q7LZ71: 1bj3 1j34 1j35 1x2t

(-) Related Entries Specified in the PDB File

1x2t HABU IX-BP AT PH 6.5