Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF RHODOSTOMIN ARGDP MUTANT
 
Authors :  Y. T. Chang, W. Y. Jeng, J. H. Shiu, C. Y. Chen, W. J. Chuang
Date :  07 Aug 13  (Deposition) - 13 Aug 14  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Rhodostomin, Disintegrin, Integrin, Argdp, Loss-Of-Function, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. T. Chang, W. Y. Jeng, J. H. Shiu, C. Y. Chen, W. J. Chuang
Effect Of C-Terminal Proline Residue Adjacent To The Rgd Motif In Rhodostomin On Its Activity And Structure
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ZINC METALLOPROTEINASE/DISINTEGRIN
    Chains: A, B, C, D
    EC Number: 3.4.24.-
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPICZALPHAA
    Expression System Strain: X-33
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 408-475
    Gene: RHOD
    Mutation: YES
    Organism Common: MALAYAN PIT VIPER
    Organism Scientific: CALLOSELASMA RHODOSTOMA
    Organism Taxid: 8717
    Synonym: SNAKE VENOM METALLOPROTEINASE RHODOSTOXIN, SVMP, HEMORRHAGIC PROTEIN, DISINTEGRIN RHODOSTOMIN, RHO, DISINTEGRIN KISTRIN, PLATELET AGGREGATION ACTIVATION INHIBITOR

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:67 , ARG B:40BINDING SITE FOR RESIDUE SO4 B 101
2AC2SOFTWAREGLY B:30 , LEU B:31 , ARG B:46 , ASP B:63 , CYS B:64BINDING SITE FOR RESIDUE SO4 B 102
3AC3SOFTWAREARG C:46 , ALA C:48 , ARG C:49 , GLY C:50 , ASP C:51BINDING SITE FOR RESIDUE SO4 C 101
4AC4SOFTWARELYS B:43 , HOH B:212 , ASP C:15 , ALA C:16 , ARG C:22BINDING SITE FOR RESIDUE SO4 C 102
5AC5SOFTWAREARG D:46 , ALA D:48 , ARG D:49 , GLY D:50 , ASP D:51BINDING SITE FOR RESIDUE SO4 D 101
6AC6SOFTWAREPRO B:52 , PRO D:53 , ASP D:54 , ARG D:56 , HOH D:229BINDING SITE FOR RESIDUE SO4 D 102

(-) SS Bonds  (24, 24)

Asymmetric Unit
No.Residues
1A:4 -A:19
2A:6 -A:14
3A:13 -A:36
4A:27 -A:33
5A:32 -A:57
6A:45 -A:64
7B:4 -B:19
8B:6 -B:14
9B:13 -B:36
10B:27 -B:33
11B:32 -B:57
12B:45 -B:64
13C:4 -C:19
14C:6 -C:14
15C:13 -C:36
16C:27 -C:33
17C:32 -C:57
18C:45 -C:64
19D:4 -D:19
20D:6 -D:14
21D:13 -D:36
22D:27 -D:33
23D:32 -D:57
24D:45 -D:64

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:51 -Pro A:52
2Asp B:51 -Pro B:52
3Pro C:52 -Pro C:53
4Pro D:52 -Pro D:53

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M4C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M4C)

(-) Exons   (0, 0)

(no "Exon" information available for 4M4C)

(-) 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:65
                                                                                                
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................ee..ee.....eeee......eee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  4m4c A  3 ECDCSSPENPCCDAATCKLRPGAQCGEGLCCEQCKFSRAGKICRIARGDPPDDRCTGQSADCPRY 67
                                    12        22        32        42        52        62     


Chain B from PDB  Type:PROTEIN  Length:65
                                                                                                
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................ee..ee.....eeee......eee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  4m4c B  3 ECDCSSPENPCCDAATCKLRPGAQCGEGLCCEQCKFSRAGKICRIARGDPPDDRCTGQSADCPRY 67
                                    12        22        32        42        52        62     


Chain C from PDB  Type:PROTEIN  Length:65
                                                                                                
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee....ee...........ee..ee.....eee........ee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  4m4c C  3 ECDCSSPENPCCDAATCKLRPGAQCGEGLCCEQCKFSRAGKICRIARGDPPDDRCTGQSADCPRY 67
                                    12        22        32        42        52        62     


Chain D from PDB  Type:PROTEIN  Length:65
                                                                                                
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee....ee...........ee..ee.....eee........ee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  4m4c D  3 ECDCSSPENPCCDAATCKLRPGAQCGEGLCCEQCKFSRAGKICRIARGDPPDDRCTGQSADCPRY 67
                                    12        22        32        42        52        62
   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  (0, 0)

(no "SCOP Domain" information available for 4M4C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M4C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M4C)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:51 - Pro A:52   [ RasMol ]  
    Asp B:51 - Pro B:52   [ RasMol ]  
    Pro C:52 - Pro C:53   [ RasMol ]  
    Pro D:52 - Pro D:53   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 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
  4m4c
    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
  VM2RH_CALRH | P30403
    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)
  3.4.24.-
    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
  VM2RH_CALRH | P30403
    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
        VM2RH_CALRH | P30403: 1n4y 1q7i 1q7j 2ljv 2m75 2m7f 2m7h 2pjf 2pjg 2pji 3uci 4r5r 4r5u 4rqg

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4M4C)