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

(-) Description

Title :  HIGH RESOLUTION STRUCTURE DETERMINATION OF RHODOCETIN
 
Authors :  P. Paaventhan, C. G. Kong, J. S. Joseph, M. C. M. Chung, P. R. Kolatkar
Date :  10 Feb 04  (Deposition) - 01 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  C-Type Lectin; Domain Swapping, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Paaventhan, C. G. Kong, J. S. Joseph, M. C. M. Chung, P. R. Kolatkar
Structure Of Rhodocetin Reveals Noncovalently Bound Heterodimer Interface
Protein Sci. V. 14 169 2005
PubMed-ID: 15576563  |  Reference-DOI: 10.1110/PS.04945605
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHODOCETIN ALPHA SUBUNIT
    Chains: A
    Organism Common: MALAYAN PIT VIPER
    Organism Scientific: CALLOSELASMA RHODOSTOMA
    Organism Taxid: 8717
    Other Details: ORGANISM NAME SYNONYM: AGKISTRODON RHODOSTOMA
 
Molecule 2 - RHODOCETIN BETA SUBUNIT
    Chains: B
    Organism Common: MALAYAN PIT VIPER
    Organism Scientific: CALLOSELASMA RHODOSTOMA
    Organism Taxid: 8717
    Other Details: ORGANISM NAME SYNONYM: AGKISTRODON RHODOSTOMA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1SB2)

(-) Sites  (0, 0)

(no "Site" information available for 1SB2)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:2 -A:13
2A:30 -A:127
3A:102 -A:119
4B:4 -B:15
5B:32 -B:123
6B:98 -B:115

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SB2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SLEA_CALRH_001 *I63KSLEA_CALRH  ---  ---AI63K
2UniProtVAR_SLEA_CALRH_002 *L70KSLEA_CALRH  ---  ---AL70K
3UniProtVAR_SLEB_CALRH_001 *E88DSLEB_CALRH  ---  ---BE88D
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLEA_CALRH9-128  1A:9-128
SLEB_CALRH11-124  1B:11-124

(-) Exons   (0, 0)

(no "Exon" information available for 1SB2)

(-) 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:132
 aligned with SLEA_CALRH | P81397 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  
           SLEA_CALRH     1 DCPDGWSSTKSYCYRPFKEKKTWEEAERFCTEQEKEAHLVSMENRLEAVFVDMVMENNFENKIYRSWIGLKIENKGQRSNLEWSDGSSISYENLYEPYMEKCFLMDHQSGLPKWHTADCEEKNVFMCKFQLP 132
               SCOP domains d1sb2a1 A:1-132 Snake coagglutinin alpha chain                                                                                       SCOP domains
               CATH domains 1sb2A00 A:1-132 Mannose-Binding Protein A, subunit A                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......ee...eeeeeeeeeehhhhhhhhhhh.....ee....hhhhhhhhhhhhhhhh....eeeeeeeeee.......eee................eeeeeeee.....eeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------K------K-------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------C_TYPE_LECTIN_2  PDB: A:9-128 UniProt: 9-128                                                                            ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sb2 A   1 DCPDGWSSTKSYCYRPFKEKKTWEEAERFCTEQEKEAHLVSMENRLEAVFVDMVMENNFENKIYRSWIGLKIENKGQRSNLEWSDGSSISYENLYEPYMEKCFLMDHQSGLPKWHTADCEEKNVFMCKFQLP 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain B from PDB  Type:PROTEIN  Length:124
 aligned with SLEB_CALRH | P81398 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
           SLEB_CALRH     2 FRCPTTWSASKLYCYKPFKEKKTWIEAERFCAKQAENGHLVSIGSAAEADFLDLVIVVNFDKQRYRAWTGLTERNLKWTNGASVSYENLYEPYIRKCFVVQPWEGKSKWYKADCEEKNAFLCKFPKP 128
               SCOP domains d1sb2b1 B:2-128 Snake coagglutinin beta chain                                                                                   SCOP domains
               CATH domains 1sb2B00 B:2-128 Mannose-Binding Protein A, subunit A                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee...eeeeeeeeeehhhhhhhhhhhhh...ee....hhhhhhhhhhhhhhhh---...eeeeeee.......................eeeeeee..eeeeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------D---------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------C_TYPE_LECTIN_2  PDB: B:11-124 UniProt: 11-124                                                                    ---- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sb2 B   2 FRCPTTWSASKLYCYKPFKEKKTWIEAERFCAKQAENGHLVSIGSAAEADFLDLVIVVNF---RYRAWTGLTERNLKWTNGASVSYENLYEPYIRKCFVVQPWEGKSKWYKADCEEKNAFLCKFPKP 128
                                    11        21        31        41        51        61   |    71        81        91       101       111       121       
                                                                                      61  65
   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
(-)
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 1SB2)

(-) Gene Ontology  (1, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SLEA_CALRH | P81397)
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   (SLEB_CALRH | P81398)
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
(no "Ligands, Modified Residues, Ions" information available for 1sb2)
 
  Sites
(no "Sites" information available for 1sb2)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1sb2)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1sb2
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SLEA_CALRH | P81397
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SLEB_CALRH | P81398
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SLEA_CALRH | P81397
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SLEB_CALRH | P81398
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SLEA_CALRH | P81397: 3gpr
        SLEB_CALRH | P81398: 3gpr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1SB2)