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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FAMILY PROTEIN FROM BABESIA BOVIS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  09 Sep 09  (Deposition) - 22 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Niaid, Ssgcid, Seattle Structural Genomics Center For Infectious Disease, Babesiosis, Parasitic Protozoan, Blood Disease, Hemolytic Disease, Piroplasmosis, Texas Cattle Fever, Tick Fever, Nantucket Fever, Redwater Fever, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. E. Edwards, B. L. Staker, Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of Nucleoside Diphosphate Kinase Family Protein From Babesia Bovis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE FAMILY PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: BG1961
    Gene: BBOV_III005290
    Organism Scientific: BABESIA BOVIS
    Organism Taxid: 484906
    Strain: T2BO

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC
Biological Unit 2 (1x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 13)

Asymmetric Unit (1, 13)
No.NameCountTypeFull Name
1SO413Ligand/IonSULFATE ION
Biological Unit 1 (1, 26)
No.NameCountTypeFull Name
1SO426Ligand/IonSULFATE ION
Biological Unit 2 (1, 13)
No.NameCountTypeFull Name
1SO413Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:39 , SER A:66 , HIS A:67BINDING SITE FOR RESIDUE SO4 A 149
02AC2SOFTWARELYS A:31 , ARG A:141 , GLY A:144 , HOH A:214BINDING SITE FOR RESIDUE SO4 A 150
03AC3SOFTWAREARG A:15 , MET C:27 , ILE C:147BINDING SITE FOR RESIDUE SO4 A 151
04AC4SOFTWARELYS A:9 , TYR A:49 , HIS A:115 , HOH A:157BINDING SITE FOR RESIDUE SO4 A 152
05AC5SOFTWAREGLU A:26 , ARG B:15BINDING SITE FOR RESIDUE SO4 B 149
06AC6SOFTWARELYS B:31 , ARG B:141 , GLY B:144 , HOH B:180BINDING SITE FOR RESIDUE SO4 B 150
07AC7SOFTWAREHIS B:39 , SER B:66 , HIS B:67BINDING SITE FOR RESIDUE SO4 B 151
08AC8SOFTWARELYS B:9 , TYR B:49 , HIS B:115BINDING SITE FOR RESIDUE SO4 B 152
09AC9SOFTWAREGLU B:26 , MET B:27 , ILE B:147 , ARG C:15BINDING SITE FOR RESIDUE SO4 C 149
10BC1SOFTWARELYS C:31 , ARG C:141 , GLY C:144 , TYR C:148 , HOH C:184 , HOH C:187BINDING SITE FOR RESIDUE SO4 C 150
11BC2SOFTWAREHIS C:39 , SER C:66 , HIS C:67BINDING SITE FOR RESIDUE SO4 C 151
12BC3SOFTWARETHR C:41 , MET C:42BINDING SITE FOR RESIDUE SO4 C 152
13BC4SOFTWARELYS C:9 , TYR C:49 , HIS C:115 , HOH C:155BINDING SITE FOR RESIDUE SO4 C 153

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JS9)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:68 -Pro A:69
2Gly B:68 -Pro B:69
3Gly C:68 -Pro C:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JS9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JS9)

(-) Exons   (0, 0)

(no "Exon" information available for 3JS9)

(-) 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:148
 aligned with A7ANF8_BABBO | A7ANF8 from UniProtKB/TrEMBL  Length:148

    Alignment length:148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        
         A7ANF8_BABBO     1 MERTYIMVKPDGVQRGLIGEILKRFEMKGLKLIAAKFEHPTMDVVAQHYCEHKDKPFFKDLCDFISHGPVFCMIWEGPEAIKIGRNLVGLTSPVESAAGTIRGDFGVVKNFNIVHASSSAEDAARECALWFTPEQLVTWERSVGGWIY 148
               SCOP domains d3js9a_ A: automated matches                                                                                                                         SCOP domains
               CATH domains 3js9A00 A:1-148  [code=3.30.70.141, no name defined]                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhhhh.eeeeeeee.hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3js9 A   1 MERTYIMVKPDGVQRGLIGEILKRFEMKGLKLIAAKFEHPTMDVVAQHYCEHKDKPFFKDLCDFISHGPVFCMIWEGPEAIKIGRNLVGLTSPVESAAGTIRGDFGVVKNFNIVHASSSAEDAARECALWFTPEQLVTWERSVGGWIY 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        


Chain B from PDB  Type:PROTEIN  Length:148
 aligned with A7ANF8_BABBO | A7ANF8 from UniProtKB/TrEMBL  Length:148

    Alignment length:148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        
         A7ANF8_BABBO     1 MERTYIMVKPDGVQRGLIGEILKRFEMKGLKLIAAKFEHPTMDVVAQHYCEHKDKPFFKDLCDFISHGPVFCMIWEGPEAIKIGRNLVGLTSPVESAAGTIRGDFGVVKNFNIVHASSSAEDAARECALWFTPEQLVTWERSVGGWIY 148
               SCOP domains d3js9b_ B: automated matches                                                                                                                         SCOP domains
               CATH domains 3js9B00 B:1-148  [code=3.30.70.141, no name defined]                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhhhh.eeeeeeee.hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3js9 B   1 MERTYIMVKPDGVQRGLIGEILKRFEMKGLKLIAAKFEHPTMDVVAQHYCEHKDKPFFKDLCDFISHGPVFCMIWEGPEAIKIGRNLVGLTSPVESAAGTIRGDFGVVKNFNIVHASSSAEDAARECALWFTPEQLVTWERSVGGWIY 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        


Chain C from PDB  Type:PROTEIN  Length:148
 aligned with A7ANF8_BABBO | A7ANF8 from UniProtKB/TrEMBL  Length:148

    Alignment length:148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        
         A7ANF8_BABBO     1 MERTYIMVKPDGVQRGLIGEILKRFEMKGLKLIAAKFEHPTMDVVAQHYCEHKDKPFFKDLCDFISHGPVFCMIWEGPEAIKIGRNLVGLTSPVESAAGTIRGDFGVVKNFNIVHASSSAEDAARECALWFTPEQLVTWERSVGGWIY 148
               SCOP domains d3js9c_ C: automated matches                                                                                                                         SCOP domains
               CATH domains 3js9C00 C:1-148  [code=3.30.70.141, no name defined]                                                                                                 CATH domains
           Pfam domains (1) -NDK-3js9C01 C:2-136                                                                                                                    ------------ Pfam domains (1)
           Pfam domains (2) -NDK-3js9C02 C:2-136                                                                                                                    ------------ Pfam domains (2)
           Pfam domains (3) -NDK-3js9C03 C:2-136                                                                                                                    ------------ Pfam domains (3)
         Sec.struct. author .eeeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhhhh.eeeeeeee.hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3js9 C   1 MERTYIMVKPDGVQRGLIGEILKRFEMKGLKLIAAKFEHPTMDVVAQHYCEHKDKPFFKDLCDFISHGPVFCMIWEGPEAIKIGRNLVGLTSPVESAAGTIRGDFGVVKNFNIVHASSSAEDAARECALWFTPEQLVTWERSVGGWIY 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: NDK] (40)
(-)
Family: NDK (40)
(-)
Babesia bovis (1)
1aNDK-3js9C01C:2-136
1bNDK-3js9C02C:2-136
1cNDK-3js9C03C:2-136

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (A7ANF8_BABBO | A7ANF8)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0004550    nucleoside diphosphate kinase activity    Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
biological process
    GO:0006241    CTP biosynthetic process    The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate.
    GO:0006183    GTP biosynthetic process    The chemical reactions and pathways resulting in the formation of GTP, guanosine triphosphate.
    GO:0006228    UTP biosynthetic process    The chemical reactions and pathways resulting in the formation of UTP, uridine (5'-)triphosphate.
    GO:0006165    nucleoside diphosphate phosphorylation    The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:68 - Pro A:69   [ RasMol ]  
    Gly B:68 - Pro B:69   [ RasMol ]  
    Gly C:68 - Pro C:69   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  3js9
    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
  A7ANF8_BABBO | A7ANF8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  A7ANF8_BABBO | A7ANF8
    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 3JS9)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3JS9)