Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
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 EOXYCYTIDINE TRIPHOSPHATE DEAMINASE FROM ANAPLASMA PHAGOCYTOPHILUM AT 2.1A RESOLUTION
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  09 Nov 09  (Deposition) - 24 Nov 09  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Ssgcid, Nih, Niaid, Sbri, Uw, Decode, Deoxycytidine Triphosphate Deaminase, Anaplasma Phagocytophilum, Iodide Phasing, Hydrolase, Nucleotide Metabolism, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Abendroth, A. S. Gardberg, J. I. Robinson, J. S. Christensen, B. L. Staker, P. J. Myler, L. J. Stewart, T. E. Edwards
Sad Phasing Using Iodide Ions In A High-Throughput Structural Genomics Environment.
J. Struct. Funct. Genom. V. 12 83 2011
PubMed-ID: 21359836  |  Reference-DOI: 10.1007/S10969-011-9101-7

(-) Compounds

Molecule 1 - DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
    Chains: A, B
    EC Number: 3.5.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DCD, APH_0130
    Organism Scientific: ANAPLASMA PHAGOCYTOPHILUM
    Organism Taxid: 212042
    Strain: HZ
    Synonym: DCTP DEAMINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 16)

Asymmetric Unit (1, 16)
No.NameCountTypeFull Name
1IOD16Ligand/IonIODIDE ION
Biological Unit 1 (1, 48)
No.NameCountTypeFull Name
1IOD48Ligand/IonIODIDE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:77BINDING SITE FOR RESIDUE IOD A 188
02AC2SOFTWARELYS A:50 , HOH A:251 , HOH A:270BINDING SITE FOR RESIDUE IOD A 189
03AC3SOFTWAREGLY A:106BINDING SITE FOR RESIDUE IOD A 190
04AC4SOFTWARETYR A:129BINDING SITE FOR RESIDUE IOD A 191
05AC5SOFTWAREMET B:4BINDING SITE FOR RESIDUE IOD B 187
06AC6SOFTWARELYS B:50 , LYS B:89BINDING SITE FOR RESIDUE IOD B 188
07AC7SOFTWAREPHE B:77BINDING SITE FOR RESIDUE IOD B 189
08AC8SOFTWAREGLY B:106BINDING SITE FOR RESIDUE IOD B 190
09AC9SOFTWAREGLN B:67BINDING SITE FOR RESIDUE IOD B 192
10BC1SOFTWAREHOH A:299 , ARG B:73 , ILE B:79BINDING SITE FOR RESIDUE IOD B 193
11BC2SOFTWAREARG A:73 , ILE A:79BINDING SITE FOR RESIDUE IOD A 193

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KM3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:20 -Pro A:21
2Ser B:20 -Pro B:21

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KM3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KM3)

(-) Exons   (0, 0)

(no "Exon" information available for 3KM3)

(-) 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:161
 aligned with DCD_ANAPZ | Q2GLJ4 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:161
                               1                                                                                                                                                             
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157 
            DCD_ANAPZ     - ---MSVMPDHWIKERALKDGMISPFVDHKEGTGVLSYGLSSYGYDARLDNKFKIFANTHSVVVDPKNFSQDSFVDREGDFCIIPPNSFMLAKTVEYFNIPRDVMVVCVGKSTYARCGIVVNVTPLEPGWSGYVTLEFSNTSPLPVKVYAFEGACQFLFFSG 158
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhhhhhhhhhhh.ee..............eee..eeeeeeeeeeeee.............hhh.eeeee..eeee...eeeeeeeeeeee....eeeeee.hhhhhh..eee.........eeeeeeeeee.....eeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3km3 A  -2 PGSMSVMPDHWIKERALKDGMISPFVDHKEGTGVLSYGLSSYGYDARLDNKFKIFANTHSVVVDPKNFSQDSFVDREGDFCIIPPNSFMLAKTVEYFNIPRDVMVVCVGKSTYARCGIVVNVTPLEPGWSGYVTLEFSNTSPLPVKVYAFEGACQFLFFSG 158
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157 


Chain B from PDB  Type:PROTEIN  Length:156
 aligned with DCD_ANAPZ | Q2GLJ4 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:158
                             1                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149        
            DCD_ANAPZ     - -MSVMPDHWIKERALKDGMISPFVDHKEGTGVLSYGLSSYGYDARLDNKFKIFANTHSVVVDPKNFSQDSFVDREGDFCIIPPNSFMLAKTVEYFNIPRDVMVVCVGKSTYARCGIVVNVTPLEPGWSGYVTLEFSNTSPLPVKVYAFEGACQFLFFS 157
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhh..ee........--....eee..eeeeeeeeeeeee.............hhh.eeeee..eeee...eeeeeeeeeeee.....eeeeeehhhhhh..eee.........eeeeeeeeee.....eeee...eeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3km3 B   0 SMSVMPDHWIKERALKDGMISPFVDHKEG--VLSYGLSSYGYDARLDNKFKIFANTHSVVVDPKNFSQDSFVDREGDFCIIPPNSFMLAKTVEYFNIPRDVMVVCVGKSTYARCGIVVNVTPLEPGWSGYVTLEFSNTSPLPVKVYAFEGACQFLFFS 157
                                     9        19        |- |      39        49        59        69        79        89        99       109       119       129       139       149        
                                                       28 31
   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 3KM3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KM3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3KM3)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DCD_ANAPZ | Q2GLJ4)
molecular function
    GO:0008829    dCTP deaminase activity    Catalysis of the reaction: dCTP + H2O = dUTP + NH3.
    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.
biological process
    GO:0006253    dCTP catabolic process    The chemical reactions and pathways resulting in the breakdown of dCTP, deoxycytidine triphosphate.
    GO:0006226    dUMP biosynthetic process    The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).
    GO:0006229    dUTP biosynthetic process    The chemical reactions and pathways resulting in the formation of dUTP, deoxyuridine (5'-)triphosphate.
    GO:0009117    nucleotide metabolic process    The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
    GO:0009220    pyrimidine ribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

 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
    IOD  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:20 - Pro A:21   [ RasMol ]  
    Ser B:20 - Pro B:21   [ 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
  3km3
    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
  DCD_ANAPZ | Q2GLJ4
    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)
  3.5.4.13
    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
  DCD_ANAPZ | Q2GLJ4
    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 3KM3)

(-) Related Entries Specified in the PDB File

3k9g 3kw3 3luz 3men 3njb 3o2e 3oib 3p96 3pfd 3pm6