PDBsum entry 2dya

Transferase

PDB id: 2dya

Contents

Protein chains

154 a.a. *

Ligands

ADP ×2

Metals

_MG ×2

_CL ×4

Waters ×334

* Residue conservation analysis

PDB id:

2dya

Name:

Transferase

Title:

Crystal structure of complex between adenine nucleotide and nucleoside diphosphate kinase

Structure:

Nucleoside diphosphate kinase. Chain: a, b. Synonym: ndk, ndp kinase, nucleoside-2-p kinase. Engineered: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. Gene: ndk. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.77Å R-factor: 0.114 R-free: 0.169

Authors:

M.Kato-Murayama,K.Murayama,T.Terada,M.Shirouzu,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

M.Kato-Murayama et al. Crystal structure of complex between adenine nucleotide and nucleoside diphosphate kinase. To be published, .

Date:

08-Sep-06 Release date: 08-Mar-07

Protein chains

O58429  (NDK_PYRHO) -  Nucleoside diphosphate kinase from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: 157 a.a.

Struc: 154 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.4.6 - nucleoside-diphosphate kinase.
• Reaction:
  1. a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP
  2. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP

ribonucleoside 5'-diphosphate + ATP = ribonucleoside 5'-triphosphate + ADP (Bound ligand (Het Group name = ADP) corresponds exactly)

2'-deoxyribonucleoside 5'-diphosphate + ATP = 2'-deoxyribonucleoside 5'-triphosphate + ADP (Bound ligand (Het Group name = ADP) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site