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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF SEMET TDP2 FROM CAENORHABDITIS ELEGANS
 
Authors :  K. Shi, K. Kurahashi, H. Aihara
Date :  07 May 12  (Deposition) - 31 Oct 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  5'-Tyrosyl Dna Phosphodiesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Shi, K. Kurahashi, R. Gao, S. E. Tsutakawa, J. A. Tainer, Y. Pommier, H. Aihara
Structural Basis For Recognition Of 5'-Phosphotyrosine Adducts By Tdp2.
Nat. Struct. Mol. Biol. V. 19 1372 2012
PubMed-ID: 23104058  |  Reference-DOI: 10.1038/NSMB.2423

(-) Compounds

Molecule 1 - 5'-TYROSYL-DNA PHOSPHODIESTERASE
    Chains: A
    EC Number: 3.1.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 21-362
    Gene: Y63D3A.4
    Organism Common: NEMATODE
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Synonym: 5'-TYR-DNA PHOSPHODIESTERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 34)
No.NameCountTypeFull Name
1GOL16Ligand/IonGLYCEROL
2MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:158 , HIS A:232 , SER A:235 , ASP A:271 , ASN A:273 , TRP A:303 , ASP A:352 , HIS A:353BINDING SITE FOR RESIDUE GOL A 401
2AC2SOFTWARELYS A:175 , ILE A:176 , TYR A:177BINDING SITE FOR RESIDUE GOL A 402
3AC3SOFTWAREGLY A:285 , TRP A:326 , GLY A:328 , LEU A:330BINDING SITE FOR RESIDUE GOL A 403
4AC4SOFTWAREASN A:150 , PRO A:151 , ASP A:152 , SER A:192BINDING SITE FOR RESIDUE GOL A 404
5AC5SOFTWAREMSE A:110 , THR A:111 , ALA A:112 , PRO A:329BINDING SITE FOR RESIDUE GOL A 405
6AC6SOFTWAREHOH A:541BINDING SITE FOR RESIDUE GOL A 406
7AC7SOFTWARETYR A:178 , HIS A:200BINDING SITE FOR RESIDUE GOL A 407
8AC8SOFTWAREALA A:292 , LYS A:332 , VAL A:333BINDING SITE FOR RESIDUE GOL A 408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F1I)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Mse A:110 -Thr A:111

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F1I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F1I)

(-) Exons   (0, 0)

(no "Exon" information available for 4F1I)

(-) 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:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................hhhhhhhhhhhh..hhhhhhhhhhh..hhhhhh..eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhh.eeeee.......eeeeeee..eeeeeeeeee........eeeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhh.......eehhhhh..hhhhh..ee.............ee..eeeeee....eeeeeee................eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f1i A  21 EDSEVEIEILDEPEQGKLSmSDEQKLHEFAIITATDEAFAQSILQDVDWDLKKALDVFYGSEAFAEARSAAVmGVmTAEDLKGFEVSVmSWNIDGLDGRSLLTRmKAVAHIVKNVNPDILFLQEVVDRDLAPIDKLQSLYKIYYSNKGCQYYTAILVSKmFDVEKHDVIHFQNSGmYRTLQILEGSIGGLKVFLLNTHLESTREHRPQRCAQFGFCmDKVREIIAQNPGALVFFGGDLNLRDEEVSRVPDGVKDAWEAAGSDNKTKFTWDTFKNDNKQGFHGAKmRFDRLYWSGPLDKVKFTLEGRQRIRSCLCFPSDHWAINATFFA 362
                                    30       |43        53        63        73        83        93  |||| 114       124       134    |  144       154       164       174       184       194       204     | 214       224       234       244      |254       264       274       284       294       304       314    |  324       334       344       354        
                                            38||                                                   96-MSE         123-MSE         139-MSE                                                194-MSE         210-MSE                                  251-MSE                                                             319-MSE                                       
                                             42|                                                    97||                                                                                                                                                                                                                                                            
                                              43-MSE                                                109|                                                                                                                                                                                                                                                            
                                                                                                     110-MSE
   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 4F1I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F1I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F1I)

(-) Gene Ontology  (7, 7)

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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Mse A:110 - Thr A:111   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  4f1i
    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
  TYDP2_CAEEL | Q9XWG3
    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)
  3.1.4.-
    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
  TYDP2_CAEEL | Q9XWG3
    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
        TYDP2_CAEEL | Q9XWG3: 4fva 4gew

(-) Related Entries Specified in the PDB File

4f1h 4fpv 4fva 4gew