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

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

Coordinates

PDB Format Compare

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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.71 Hydrogen bonds: A:K.19, A:Y.59, A:R.112, A:N.122 Water bridges: A:K.19, A:R.95, A:R.95, A:R.112, A:N.122 Salt bridges: A:K.19, A:K.19, A:R.95, A:R.112, A:H.125 CIT.3: 7 residues within 4Å: Chain B: K.19, Y.59, L.71, T.101, R.112, N.122, H.125 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.19, B:R.112, B:N.122 Water bridges: B:H.62, B:R.95, B:R.112, B:H.125 Salt bridges: B:K.19, B:K.19, B:R.112, B:H.125

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

EDO.2: 4 residues within 4Å: Chain A: F.58, L.135, E.136, Y.139 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.132 EDO.4: 5 residues within 4Å: Chain B: E.57, F.58, L.135, E.136, Y.139 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.57, B:E.136

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
I

B
J

Nucleoside diphosphate kinase

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