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(-) Description

Title :  THE STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE (NDK) FROM BURKHOLDERIA THAILANDENSIS BOUND TO DEOXYADENOSINE MONOPHOSPHATE
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  09 Apr 12  (Deposition) - 09 May 12  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Damp, Niaid, National Institute Of Allergy And Infectious Diseases, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, L. A. Gallagher, R. Patrapuvich, M. C. Clifton, A. S. Gardberg, T. E. Edwards, B. Armour, D. W. Begley, S. H. Dieterich, D. M. Dranow, J. Abendroth, J. W. Fairman, D. Fox, B. L. Staker, I. Phan, A. Gillespie, R. Choi, S. Nakazawa-Hewitt, M. T. Nguyen, A. Napuli, L. Barrett, G. W. Buchko, R. Stacy, P. J. Myler, L. J. Stewart, C. Manoil W. C. Van Voorhis
Combining Functional And Structural Genomics To Sample The Essential Burkholderia Structome.
Plos One V. 8 53851 2013
PubMed-ID: 23382856  |  Reference-DOI: 10.1371/JOURNAL.PONE.0053851

(-) Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE
    Chains: A, B
    EC Number: 2.7.4.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NDK, BTH_I2231
    Organism Scientific: BURKHOLDERIA THAILANDENSIS
    Organism Taxid: 271848
    Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301
    Synonym: NDK, NDP KINASE, NUCLEOSIDE-2-P KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2DA1Ligand/Ion2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
3DMS2Ligand/IonDIMETHYL SULFOXIDE
4EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:11 , TYR A:51 , HIS A:117BINDING SITE FOR RESIDUE CL A 201
2AC2SOFTWAREGLU A:4 , ARG A:5 , PRO A:122 , ALA A:125 , ARG A:126 , ILE A:129 , DA A:203 , HOH A:430BINDING SITE FOR RESIDUE DMS A 202
3AC3SOFTWAREALA A:2 , LEU A:3 , DMS A:202 , HOH A:349 , HOH A:429 , HOH A:430 , PHE B:59 , LEU B:63 , THR B:93 , ASP B:112 , HOH B:399BINDING SITE FOR RESIDUE DA A 203
4AC4SOFTWARELYS B:11 , TYR B:51 , HIS B:117BINDING SITE FOR RESIDUE CL B 201
5AC5SOFTWAREPHE B:50 , TYR B:51 , VAL B:53 , HIS B:54 , GLU B:128BINDING SITE FOR RESIDUE EDO B 202
6AC6SOFTWAREGLU B:4 , ARG B:5 , PRO B:122 , ARG B:126BINDING SITE FOR RESIDUE DMS B 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EK2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EK2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EK2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EK2)

(-) Exons   (0, 0)

(no "Exon" information available for 4EK2)

(-) 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:142
                                                                                                                                                                              
               SCOP domains d4ek2a_ A: automated matches                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeeeehhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ek2 A   0 SMALERTLSIIKPDAVAKNVIGQIYSRFENAGLKIVAARMAHLSRADAEKFYAVHAERPFFKDLVEFMISGPVMIQVLEGEDAILKNRDLMGATDPKKAEKGTIRADFADSIDANAVHGSDAPETARVEIAFFFPEMNVYSR 141
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139  


Chain B from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains d4ek2b_ B: automated matches                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..........hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ek2 B   2 ALERTLSIIKPDAVAKNVIGQIYSRFENAGLKIVAARMAHLSRADAEKFYAVHAERPFFKDLVEFMISGPVMIQVLEGEDAILKNRDLMGATDPKKAEKGTIRADFADSIDANAVHGSDAPETARVEIAFFFPEMNVYSR 141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
   Legend:   → Mismatch (orange background)
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  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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EK2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EK2)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NDK_BURTA | Q2SWE7: 4dut 4hr2

(-) Related Entries Specified in the PDB File

4dut SAME PROTEIN BOUND TO DEOXYADENOSINE MONOPHOSPHATE RELATED ID: SSGCID-BUTHA.00438.A RELATED DB: TARGETTRACK