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(-) Description

Title :  CRYSTAL STRUCTURE (TYPE-2) OF DTMP KINASE (ST1543) FROM SULFOLOBUS TOKODAII STRAIN7
 
Authors :  A. Biswas, J. Jeyakanthan, K. Sekar, S. Kuramitsu, S. Yokoyama
Date :  13 Dec 13  (Deposition) - 24 Dec 14  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Biswas, J. Jeyakanthan, K. Sekar
Insight Into Substrate Binding Mechanism In Thymidylate Kinase Based On Intrinsic Dynamics Of The Active Site
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE THYMIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: STK_15430, TMK, TMK STK_15430
    Organism Scientific: SULFOLOBUS TOKODAII
    Organism Taxid: 273063
    Strain: STRAIN7
    Synonym: DTMP KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 22)

Asymmetric/Biological Unit (7, 22)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2EDO8Ligand/Ion1,2-ETHANEDIOL
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4PEG8Ligand/IonDI(HYDROXYETHYL)ETHER
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6PGE1Ligand/IonTRIETHYLENE GLYCOL
7PO42Ligand/IonPHOSPHATE ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:35 , THR A:37 , SER A:41 , SER A:42 , ASP A:43 , ARG A:74 , TYR A:78 , HOH A:473NULL
02AC2SOFTWAREGLY A:14 , SER A:15 , GLY A:16 , LYS A:17 , SER A:18 , HOH A:446NULL
03AC3SOFTWAREVAL A:107 , ASP A:108 , TRP A:111 , HOH A:461 , HOH A:501 , SER B:117 , PHE B:118NULL
04AC4SOFTWARETRP A:39 , SER A:42 , HIS A:67 , ASP A:70 , ARG A:74 , HOH A:429 , HOH A:488NULL
05AC5SOFTWARELYS A:195 , ARG A:202NULL
06AC6SOFTWARESER A:103 , LEU A:171 , GLU A:174 , VAL A:175 , LYS A:178NULL
07AC7SOFTWARETYR A:96 , PRO A:122 , ASP A:123 , ILE A:124 , THR A:125 , GLU A:183 , ASN A:184 , PG4 B:301NULL
08AC8SOFTWAREARG A:129 , VAL A:130 , ASP A:189 , HOH A:433NULL
09AC9SOFTWAREARG A:129 , HOH A:483NULL
10BC1SOFTWAREARG A:93 , ARG A:101 , GLN A:149 , TYR A:168 , HOH A:404 , HOH A:463 , HOH A:480NULL
11BC2SOFTWARELYS A:140 , GLN A:200NULL
12BC3SOFTWARELYS A:121 , GLU A:183 , PEG A:307 , ARG B:129 , ASP B:177 , HOH B:404NULL
13BC4SOFTWARELYS A:113 , SER B:103 , GLU B:174 , LYS B:178NULL
14BC5SOFTWAREILE B:12 , ASP B:13 , GLY B:14 , SER B:15 , GLY B:16 , LYS B:17 , SER B:18NULL
15BC6SOFTWARESER A:117 , ASP B:108 , TRP B:111 , 1PE B:311NULL
16BC7SOFTWARESER A:131 , GLY A:170 , THR A:173 , GLU A:174 , LYS B:53 , ASP B:56NULL
17BC8SOFTWAREPRO B:132 , GLY B:170 , THR B:173 , HOH B:402NULL
18BC9SOFTWARELEU B:58 , PHE B:63 , ASP B:154NULL
19CC1SOFTWARESER B:117 , PHE B:118NULL
20CC2SOFTWAREHOH B:450NULL
21CC3SOFTWAREPHE B:71 , TYR B:94 , ARG B:101 , TYR B:116NULL
22CC4SOFTWARELYS A:114 , SER A:117 , ASP B:110 , TRP B:111 , GLU B:174 , PEG B:304 , HOH B:431NULL

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NZY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NZY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NZY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NZY)

(-) Exons   (0, 0)

(no "Exon" information available for 4NZY)

(-) 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:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh...hhhhhhhhh.......eeeeee.hhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nzy A   3 KGVLIAFEGIDGSGKSSQATLLKDWIELKRDVYLTEWNSSDWIHDIIKEAKKKDLLTPLTFSLIHATDFSDRYERYILPMLKSGFIVISDRYIYTAYARDSVRGVDIDWVKKLYSFAIKPDITFYIRVSPDIALERIKKSKRKIKPQEAGADIFPGLSPEEGFLKYQGLITEVYDKLVKDENFIVIDGTKTPKEIQIQIRKFVGELIDN 211
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202         


Chain B from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh....eee..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh..hhhhhhhhh.......eeeeee.hhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nzy B   3 KGVLIAFEGIDGSGKSSQATLLKDWIELKRDVYLTSSDWIHDIIKEAKKKDLLTPLTFSLIHATDFSDRYERYILPMLKSGFIVISDRYIYTAYARDSVRGVDIDWVKKLYSFAIKPDITFYIRVSPDIALERIKKSKRKIKPQEAGADIFPGLSPEEGFLKYQGLITEVYDKLVKDENFIVIDGTKTPKEIQIQIRKFVGELID 210
                                    12        22        32    ||  45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205     
                                                             37|                                                                                                                                                                         
                                                              41
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  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 4NZY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NZY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NZY)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  KTHY2_SULTO | Q970Q8
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 Related Entries

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        KTHY2_SULTO | Q970Q8: 2plr 4rzu 4rzx 5h70

(-) Related Entries Specified in the PDB File

2plr THE SAME PROTEIN FROM SULFOLOBUS TOKODAII IN DISALLOWED ALLOWED FORM