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 THE HUMAN TATD-DOMAIN PROTEIN 3 (TATDN3)
 
Authors :  J. R. C. Muniz, S. Puranik, T. Krojer, W. W. Yue, E. Ugochukwu, P. Filippa F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, K. L. Kavanagh, U. Oppermann
Date :  08 Dec 10  (Deposition) - 29 Dec 10  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. C. Muniz, S. Puranik, T. Krojer, W. W. Yue, E. Ugochukwu, P. Filippakopoulos, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, K. L. Kavanagh, U. Oppermann
Crystal Structure Of The Human Tatd-Domain Protein 3 (Tatdn3)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE DEOXYRIBONUCLEASE TATDN3
    Chains: A, B
    EC Number: 3.1.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: R3-PL
    Expression System Vector: PNIC28-BSA4
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 5-274
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TATD-DOMAIN PROTEIN 3

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2NI2Ligand/IonNICKEL (II) ION
3PO42Ligand/IonPHOSPHATE ION
4ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2NI-1Ligand/IonNICKEL (II) ION
3PO42Ligand/IonPHOSPHATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:107 , HIS A:147 , HIS A:170 , ZN A:1274 , PO4 A:1275BINDING SITE FOR RESIDUE ZN A1273
2AC2SOFTWAREHIS A:12 , HIS A:14 , GLU A:107 , HIS A:170 , ASP A:218 , ZN A:1273 , PO4 A:1275BINDING SITE FOR RESIDUE ZN A1274
3AC3SOFTWAREHIS A:12 , HIS A:14 , GLU A:44 , HIS A:70 , GLU A:107 , HIS A:147 , HIS A:170 , ASP A:218 , ZN A:1273 , ZN A:1274 , HOH A:2028BINDING SITE FOR RESIDUE PO4 A1275
4AC4SOFTWAREARG A:229 , GLU A:231 , HOH A:2022 , GLU B:225BINDING SITE FOR RESIDUE NI A1276
5AC5SOFTWAREHIS B:12 , HIS B:14 , GLU B:107 , HIS B:170 , ASP B:218 , ZN B:1274 , PO4 B:1275BINDING SITE FOR RESIDUE ZN B1273
6AC6SOFTWAREGLU B:107 , HIS B:147 , HIS B:170 , ZN B:1273 , PO4 B:1275BINDING SITE FOR RESIDUE ZN B1274
7AC7SOFTWAREHIS B:14 , GLU B:44 , HIS B:70 , GLU B:107 , HIS B:147 , ASP B:218 , ZN B:1273 , ZN B:1274BINDING SITE FOR RESIDUE PO4 B1275
8AC8SOFTWAREGLU A:225 , ARG B:229 , GLU B:231 , HOH B:2007 , HOH B:2021BINDING SITE FOR RESIDUE NI B1276
9AC9SOFTWAREASP B:25 , ARG B:58 , TYR B:59BINDING SITE FOR RESIDUE EDO B1277

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y1H)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:219 -Pro A:220
2Ser B:219 -Pro B:220

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y1H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y1H)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y1H)

(-) 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:262
 aligned with TATD3_HUMAN | Q17R31 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:269
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263         
          TATD3_HUMAN     4 AGVGLVDCHCHLSAPDFDRDLDDVLEKAKKANVVALVAVAEHSGEFEKIMQLSERYNGFVLPCLGVHPVQGLPPEDQRSVTLKDLDVALPIIENYKDRLLAIGEVGLDFSPRFAGTGEQKEEQRQVLIRQIQLAKRLNLPVNVHSRSAGRPTINLLQEQGAEKVLLHAFDGRPSVAMEGVRAGYFFSIPPSIIRSGQKQKLVKQLPLTSICLETDSPALGPEKQVRNEPWNISISAEYIAQVKGISVEEVIEVTTQNALKLFPKLRHLL 272
               SCOP domains d2y1ha_ A: automated matches                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...hhhhh.hhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhh...eeeee......-------...hhhhhhhhhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhh....eeee....hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhh.eee...............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y1h A   4 MGVGLVDCHCHLSAPDFDRDLDDVLEKAKKANVVALVAVAEHSGEFEKIMQLSERYNGFVLPCLGVHPVQ-------RSVTLKDLDVALPIIENYKDRLLAIGEVGLDFSPRFAGTGEQKEEQRQVLIRQIQLAKRLNLPVNVHSRSAGRPTINLLQEQGAEKVLLHAFDGRPSVAMEGVRAGYFFSIPPSIIRSGQKQKLVKQLPLTSICLETDSPALGPEKQVRNEPWNISISAEYIAQVKGISVEEVIEVTTQNALKLFPKLRHLL 272
                                    13        23        33        43        53        63        73       |83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263         
                                                                                                73      81                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:265
 aligned with TATD3_HUMAN | Q17R31 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:268
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264        
          TATD3_HUMAN     5 GVGLVDCHCHLSAPDFDRDLDDVLEKAKKANVVALVAVAEHSGEFEKIMQLSERYNGFVLPCLGVHPVQGLPPEDQRSVTLKDLDVALPIIENYKDRLLAIGEVGLDFSPRFAGTGEQKEEQRQVLIRQIQLAKRLNLPVNVHSRSAGRPTINLLQEQGAEKVLLHAFDGRPSVAMEGVRAGYFFSIPPSIIRSGQKQKLVKQLPLTSICLETDSPALGPEKQVRNEPWNISISAEYIAQVKGISVEEVIEVTTQNALKLFPKLRHLL 272
               SCOP domains d2y1hb_ B: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----TatD_DNase-2y1hB01 B:9-267                                                                                                                                                                                                                                         ----- Pfam domains (1)
           Pfam domains (2) ----TatD_DNase-2y1hB02 B:9-267                                                                                                                                                                                                                                         ----- Pfam domains (2)
         Sec.struct. author ...eeeeee...hhhhh.hhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhh...eeeee....ee..---..ee.hhhhhhhhhhhhhhhh....eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh....eeee....hhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhh.eee...............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y1h B   5 GVGLVDCHCHLSAPDFDRDLDDVLEKAKKANVVALVAVAEHSGEFEKIMQLSERYNGFVLPCLGVHPVQGL---DQRSVTLKDLDVALPIIENYKDRLLAIGEVGLDFSPRFAGTGEQKEEQRQVLIRQIQLAKRLNLPVNVHSRSAGRPTINLLQEQGAEKVLLHAFDGRPSVAMEGVRAGYFFSIPPSIIRSGQKQKLVKQLPLTSICLETDSPALGPEKQVRNEPWNISISAEYIAQVKGISVEEVIEVTTQNALKLFPKLRHLL 272
                                    14        24        34        44        54        64        74|   |   84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264        
                                                                                                 75  79
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y1H)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TATD3_HUMAN | Q17R31)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:219 - Pro A:220   [ RasMol ]  
    Ser B:219 - Pro B:220   [ 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
  2y1h
    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
  TATD3_HUMAN | Q17R31
    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)
  3.1.21.-
    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
  TATD3_HUMAN | Q17R31
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2Y1H)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Y1H)