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

(-) Description

Title :  ADP-DTMP BOUND CRYSTAL STRUCTURE OF THYMIDYLATE KINASE (AQ_969) FROM AQUIFEX AEOLICUS VF5
 
Authors :  A. Biswas, J. Jeyakanthan, K. Sekar
Date :  15 Mar 17  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase, Complex, Nucleotide Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Biswas, J. Jeyakanthan, K. Sekar, S. Kuramitsu, S. Yokoyama
Structural Studies Of A Hyperthermophilic Thymidylate Kinas Enzyme Reveal Conformational Sub-States Along The Reaction Coordinate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THYMIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TMK, AQ_969
    Organism Scientific: AQUIFEX AEOLICUS (STRAIN VF5)
    Organism Taxid: 224324
    Strain: VF5
    Synonym: DTMP KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2TMP2Ligand/IonTHYMIDINE-5'-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , SER A:11 , GLY A:12 , LYS A:13 , THR A:14 , THR A:15 , ARG A:139 , ARG A:145 , GLY A:176 , GLU A:177 , GLU A:178 , HOH A:323 , HOH A:339 , HOH A:357 , HOH A:376 , HOH A:388binding site for residue ADP A 201
2AC2SOFTWAREASP A:9 , GLU A:36 , ARG A:47 , PHE A:64 , ARG A:90 , THR A:95 , TYR A:98 , GLN A:99 , HOH A:323 , HOH A:339 , HOH A:359 , HOH A:363 , HOH A:397 , HOH A:402binding site for residue TMP A 202
3AC3SOFTWAREGLY B:10 , SER B:11 , GLY B:12 , LYS B:13 , THR B:14 , THR B:15 , ARG B:139 , LYS B:143 , ARG B:145 , GLY B:176 , GLU B:177 , GLU B:178 , HOH B:303 , HOH B:311 , HOH B:340 , HOH B:346 , HOH B:352 , HOH B:359 , HOH B:360 , HOH B:379binding site for residue ADP B 201
4AC4SOFTWAREASP B:9 , GLU B:36 , ARG B:47 , PHE B:64 , ARG B:90 , THR B:95 , TYR B:98 , GLN B:99 , ARG B:145 , HOH B:301 , HOH B:340 , HOH B:352 , HOH B:358 , HOH B:378 , HOH B:384 , HOH B:393 , HOH B:406binding site for residue TMP B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5XB3)

(-) Cis Peptide Bonds  (2, 3)

Asymmetric/Biological Unit
No.Residues
1Glu A:36 -Pro A:37
2Glu B:36 -Pro B:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5XB3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5XB3)

(-) Exons   (0, 0)

(no "Exon" information available for 5XB3)

(-) Sequences/Alignments

Asymmetric/Biological 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:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xb3 A   1 MLIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYREPGGTKVGEVLREILLTEELDERTELLLFEASRSKLIEEKIIPDLKRDKVVILDRFVLSTIAYQGYGKGLDVEFIKNLNEFATRGVKPDITLLLDIPVDIALRRLKEKNRFENKEFLEKVRKGFLELAKEEENVVVIDASGEEEEVFKEILRALSGVL 193
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   


Chain B from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xb3 B   1 MLIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYREPGGTKVGEVLREILLTEELDERTELLLFEASRSKLIEEKIIPDLKRDKVVILDRFVLSTIAYQGYGKGLDVEFIKNLNEFATRGVKPDITLLLDIPVDIALRRLKEKNRFENKEFLEKVRKGFLELAKEEENVVVIDASGEEEEVFKEILRALSGVLR 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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 5XB3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5XB3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5XB3)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:36 - Pro A:37   [ RasMol ]  
    Glu B:36 - Pro B:37   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  5xb3
    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
  KTHY_AQUAE | O67099
    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)
  2.7.4.9
    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
  KTHY_AQUAE | O67099
    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
        KTHY_AQUAE | O67099: 2pbr 4s2e 4s35 5h56 5h5b 5h5k 5xai 5xb2 5xb5 5xbh

(-) Related Entries Specified in the PDB File

5xai 5xb2 5xb5 5xbh