Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AA-X-BP-I, A SNAKE VENOM PROTEIN WITH THE ACTIVITY OF BINDING TO COAGULATION FACTOR X FROM AGKISTRODON ACUTUS
 
Authors :  Z. Zhu, S. Liu, X. Mo, X. Yu, Z. Liang, J. Zang, W. Zhao, M. Teng, L. Niu
Date :  18 Nov 04  (Deposition) - 07 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aa-X-Bp-I, C-Type Lectin-Like Proteins, Snake Venom, Agksitrodon Acutus, Blood Clotting (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Zhu, S. Liu, X. Mo, X. Yu, Z. Liang, J. Zang, W. Zhao, M. Teng, L. Niu
Characterizations And Crystal Structures Of Two Snake Venom Proteins With The Activity Of Binding Coagulation Factor X From Agkistrodon Acutus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AGKISACUTACIN A CHAIN
    ChainsA
    FragmentC-TYPE LECTIN CRD DOMAIN
    Organism CommonCHINESE MOCCASIN
    Organism ScientificDEINAGKISTRODON ACUTUS
    Organism Taxid36307
    SynonymAA-X-BP-I, CHAIN A
 
Molecule 2 - ANTICOAGULANT PROTEIN-B
    ChainsB
    FragmentC-TYPE LECTIN CRD DOMAIN
    Organism CommonCHINESE MOCCASIN
    Organism ScientificDEINAGKISTRODON ACUTUS
    Organism Taxid36307
    SynonymAA-X-BP-I, CHAIN B

 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:47 , GLU A:128BINDING SITE FOR RESIDUE CA A 1001
2AC2SOFTWARESER B:41 , GLN B:43 , GLU B:47 , GLU B:120BINDING SITE FOR RESIDUE CA B 1002

(-) 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 1WT9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WT9)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLAB_DEIAC32-143  1B:9-120
SLUA_DEIAC32-151  1A:9-128
SLAA_DEIAC32-151  1A:9-128
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLAB_DEIAC119-142  1B:96-119
SLUA_DEIAC125-150  1A:102-127
SLAA_DEIAC125-150  1A:102-127

(-) Exons   (0, 0)

(no "Exon" information available for 1WT9)

(-) 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 SLAA_DEIAC | Q9DEF9 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:129
                                    33        43        53        63        73        83        93       103       113       123       133       143         
           SLAA_DEIAC    24 DCSSSWSSYEGHCYKAFKQSKTWADAESFCTKQVNGGHLVSIESSGEADFVAHLIAQKIKSAKIHVWIGLRAQNKEKQCSIEWSDGSSISYENWIEEESKKCLGVHKATGFRKWENFYCEQRDPFVCEA 152
               SCOP domains d1wt9a1 A:1-129 Snake coagglutinin alpha chain                                                                                    SCOP domains
               CATH domains 1wt9A00 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.hhhh...eeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: A:9-128 UniProt: 32-151                                                                           - PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) -----------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           -- PROSITE (5)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wt9 A   1 DCSSGWSSYEGHCYKVFKQSKTWTDAESFCTKQVNGGHLVSIESSGEADFVGQLIAQKIKSAKIHVWIGLRAQNKEKQCSIEWSDGSSISYENWIEEESKKCLGVHIETGFHKWENFYCEQQDPFVCEA 129
                                    10        20        30        40        50        60        70        80        90       100       110       120         

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 d1wt9a1 A:1-129 Snake coagglutinin alpha chain                                                                                    SCOP domains
               CATH domains 1wt9A00 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.hhhh...eeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------C_TYPE_LECTIN_2  PDB: A:9-128 UniProt: 32-151                                                                           - PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) -----------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           -- PROSITE (6)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wt9 A   1 DCSSGWSSYEGHCYKVFKQSKTWTDAESFCTKQVNGGHLVSIESSGEADFVGQLIAQKIKSAKIHVWIGLRAQNKEKQCSIEWSDGSSISYENWIEEESKKCLGVHIETGFHKWENFYCEQQDPFVCEA 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 d1wt9b_ B: Snake coagglutinin beta chain                                                                                    SCOP domains
               CATH domains 1wt9B00 B:1-123 Mannose-Binding Protein A, subunit A                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhh.....ee....hhhhhhhhhhhhhhhhh..eee...........eee...............eeeeee..eeeeeeee....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
                 1wt9 B   1 DCPSDWSSYEGHCYKPFNEPKNWADAENFCTQQHTGSHLVSFQSTEEADFVVKLAFQTFDYGIFWMGLSKIWNQCNWQWSNAAMLKYTDWAEESYCVYFKSTNNKWRSITCRMIANFVCEFQA 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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WT9)

(-) Gene Ontology  (2, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SLAA_DEIAC | Q9DEF9)
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 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wt9)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1wt9
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SLAA_DEIAC | Q9DEF9
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  SLAB_DEIAC | Q9DEF8
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  SLUA_DEIAC | Q9IAM1
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SLAA_DEIAC | Q9DEF9
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SLAB_DEIAC | Q9DEF8
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SLUA_DEIAC | Q9IAM1
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SLAA_DEIAC | Q9DEF91y17
        SLAB_DEIAC | Q9DEF81iod 1y17
        SLUA_DEIAC | Q9IAM11iod

(-) Related Entries Specified in the PDB File

1iod A VARIANT OF THIS PROTEIN (D-ACUTUS-X-BP) COMPLEXED WITH GLA DOMAIN OF FACTOR X
1y17 THIS PROTEIN WITH IDENTIC RESIDUES IN CHAIN B TO THOSE OF AA-X-BP-I