SMTL ID : 4ek2.1

The structure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis bound to deoxyadenosine monophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: K.15, Y.55, H.121 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain B: K.15, Y.55, H.121 Ligand excluded by PLIP

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 7 residues within 4Å: Chain A: E.8, R.9, P.126, A.129, R.130, I.133 Ligands: DA.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.9 DMS.6: 6 residues within 4Å: Chain B: E.8, R.9, P.126, A.129, R.130, I.133 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.9

1 x DA: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

DA.3: 3 residues within 4Å: Chain A: A.6, L.7 Ligands: DMS.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.7

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 6 residues within 4Å: Chain B: F.54, Y.55, V.57, H.58, H.121, E.132 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.58 Water bridges: B:F.54, B:E.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., Combining functional and structural genomics to sample the essential Burkholderia structome. Plos One (2013)

Release Date

2012-05-09

Peptides

Nucleoside diphosphate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nucleoside diphosphate kinase

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