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(-) Description

Title :  CRYSTAL STRUCTURE OF ADP BOUND DTMP KINASE (ST1543) FROM SULFOLOBUS TOKODAII STRAIN7
 
Authors :  A. Biswas, J. Jeyakanthan, K. Sekar, S. Kuramitsu, S. Yokoyama
Date :  15 Nov 16  (Deposition) - 07 Dec 16  (Release) - 07 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase, Transferase, Rossmann Fold, Nucleotide Bound (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Biswas, J. Jeyakanthan, K. Sekar, S. Kuramitsu, S. Yokoyama
Crystal Structure Of Adp Bound Dtmp Kinase (St1543) From Sulfolobus Tokodaii Strain7
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE THYMIDYLATE KINASE
    Chains: B, A
    EC Number: 2.7.4.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TMK, STK_15430
    Organism Scientific: SULFOLOBUS TOKODAII STRAIN 7
    Organism Taxid: 273063
    Strain: 7
    Synonym: DTMP KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MG2Ligand/IonMAGNESIUM ION
4PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:14 , SER B:15 , GLY B:16 , LYS B:17 , SER B:18 , SER B:19 , ARG B:138 , LYS B:192 , THR B:193 , PRO B:194 , ILE B:197 , MG B:303 , HOH B:401 , HOH B:402binding site for residue ADP B 301
2AC2SOFTWAREASP B:108 , TRP B:111binding site for residue EDO B 302
3AC3SOFTWARESER B:18 , ASP B:92 , ADP B:301 , HOH B:401 , HOH B:402binding site for residue MG B 303
4AC4SOFTWAREASP A:13 , GLY A:14 , SER A:15 , GLY A:16 , LYS A:17 , SER A:18 , SER A:19 , ARG A:138 , SER A:142 , LYS A:192 , PRO A:194 , MG A:304binding site for residue ADP A 301
5AC5SOFTWAREPHE A:63 , ARG A:105 , ASP A:154 , PGE A:303binding site for residue EDO A 302
6AC6SOFTWAREHIS A:46 , HIS A:67 , GLN A:149 , ASP A:154 , EDO A:302binding site for residue PGE A 303
7AC7SOFTWARESER A:18 , ASP A:92 , ADP A:301 , HOH A:403binding site for residue MG A 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H70)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5H70)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H70)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H70)

(-) Exons   (0, 0)

(no "Exon" information available for 5H70)

(-) 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:205
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh...hhhhhhhhhh......eeeeee.hhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h70 A   4 GVLIAFEGIDGSGKSSQATLLKDWIELKRDVYLTEWNSDWIHDIIKEAKKKDLLTPLTFSLIHATDFSDRYERYILPMLKSGFIVISDRYIYTAYARDSVRGVDIDWVKKLYSFAIKPDITFYIRVSPDIALERIKKSKRKIKPQEAGADIFPGLSPEEGFLKYQGLITEVYDKLVKDENFIVIDGTKTPKEIQIQIRKFVGELI 209
                                    13        23        33      ||44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204     
                                                               40|                                                                                                                                                                       
                                                                42                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh...hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h70 B   3 KGVLIAFEGIDGSGKSSQATLLKDWIELKRDVYLTEWNSSDWIHDIIKEAKKKDLLTPLTFSLIHATDFSDRYERYILPMLKSGFIVISDRYIYTAYARDSVRGVDIDWVKKLYSFAIKPDITFYIRVSPDIALERIKKSKRKIKPQEAGADIFPGLSPEEGFLKYQGLITEVYDKLVKDENFIVIDGTKTPKEIQIQIRKFVGELI 209
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202
   Legend:   → Mismatch (orange background)
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    → 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 5H70)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H70)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H70)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        KTHY2_SULTO | Q970Q8: 2plr 4nzy 4rzu 4rzx

(-) Related Entries Specified in the PDB File

2plr