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(-) Description

Title :  STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE (NDK) FROM BURKHOLDERIA THAILANDENSIS BOUND TO ADP
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  26 Oct 12  (Deposition) - 07 Nov 12  (Release) - 07 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Ssgcid, Seattle Structural Genomics Center For Infectious Disease, Niaid, National Institute Of Allergy And Infectious Diseases, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Clifton, J. A. Abendroth
Structure Of Nucleoside Diphosphate Kinase (Ndk) From Burkholderia Thailandensis Bound To Adp
To Be Published
PubMed: search

(-) 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 Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:11 , HIS A:54 , PHE A:59 , LEU A:63 , ARG A:87 , THR A:93 , ARG A:104 , ILE A:111 , ASN A:114 , HOH A:715 , HOH A:731 , HOH A:738 , HOH A:760 , HOH A:772 , HOH A:805 , HOH A:815 , HOH A:839 , HOH A:848BINDING SITE FOR RESIDUE ADP A 601
2AC2SOFTWAREALA A:2 , LEU A:3 , LYS B:11 , TYR B:51 , HIS B:54 , PHE B:59 , LEU B:63 , ARG B:104 , ILE B:111 , ASN B:114 , HIS B:117 , GLY B:118 , HOH B:780 , HOH B:785 , HOH B:787BINDING SITE FOR RESIDUE ADP B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HR2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HR2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HR2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HR2)

(-) Exons   (0, 0)

(no "Exon" information available for 4HR2)

(-) 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    
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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 d4hr2a_ 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
                 4hr2 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 d4hr2b_ B: automated matches                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..........hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hr2 B   2 ALERTLSIIKPDAVAKNVIGQIYSRFENAGLKIVAARMAHLSRADAEKFYAVHAERPFFKDLVEFMISGPVMIQVLEGEDAILKNRDLMGATDPKKAEKGTIRADFADSIDANAVHGSDAPETARVEIAFFFPEMNVYSR 141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
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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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HR2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HR2)

(-) Gene Ontology  (13, 13)

Asymmetric 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 4ek2

(-) Related Entries Specified in the PDB File

4dut
4ek2 RELATED ID: SSGCID-BUTHA.00438.A RELATED DB: TARGETTRACK