SMTL ID : 5v6d.4 (7 other biounits)

Crystal structure of nucleoside diphosphate kinase from Neisseria gonorrhoeae in complex with citrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 8 residues within 4Å: Chain A: K.19, Y.59, L.71, R.95, T.101, R.112, N.122, H.125 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.19, A:R.112, A:N.122 Water bridges: A:H.62, A:R.95, A:R.95, A:R.95, A:R.112 Salt bridges: A:K.19, A:K.19, A:R.95, A:R.112, A:H.125 CIT.4: 6 residues within 4Å: Chain B: K.19, Y.59, T.101, R.112, N.122, H.125 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:K.19, B:Y.59, B:R.112, B:N.122, B:V.124 Water bridges: B:K.19, B:R.95, B:R.95, B:R.112, B:N.122 Salt bridges: B:K.19, B:K.19, B:R.95, B:R.112, B:H.125

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

EDO.2: 5 residues within 4Å: Chain A: E.57, F.58, L.135, E.136, Y.139 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.136, A:E.136 EDO.3: 5 residues within 4Å: Chain A: K.25, N.26 Chain B: E.36, E.37 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.37, B:E.37 EDO.5: 4 residues within 4Å: Chain B: F.58, L.135, E.136, Y.139 No protein-ligand interaction detected (PLIP) EDO.6: 4 residues within 4Å: Chain A: N.26 Chain B: G.39, K.41 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.39, B:K.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of nucleoside diphosphate kinase from Neisseria gonorrhoeae in complex with citrate. To be Published

Release Date

2017-04-19

Peptides

Nucleoside diphosphate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

Nucleoside diphosphate kinase

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