SMTL ID : 5kha.1

Structure of glutamine-dependent NAD+ synthetase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 14 residues within 4Å: Chain A: Y.282, F.288, M.388, S.391, N.392, L.397, G.421, Y.517, K.518 Chain B: N.377, R.381, C.412, T.413, L.414 15 PLIP interactions: 3 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:N.377, B:L.414, A:Y.282, A:S.391, A:S.391, A:N.392, A:N.392 Salt bridges: B:R.381, A:K.518, A:K.518 Water bridges: A:G.421 pi-Stacking: A:F.288, A:F.288, A:Y.517, A:Y.517 ADP.4: 16 residues within 4Å: Chain A: A.373, N.377, R.381, C.412, T.413, L.414 Chain B: Y.282, S.286, F.288, M.388, S.391, N.392, L.397, G.421, Y.517, K.518 18 PLIP interactions: 4 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:N.377, A:L.414, B:S.286, B:S.286, B:S.391, B:S.391, B:N.392, B:N.392 Water bridges: A:G.410, B:G.421, B:K.518 Salt bridges: A:R.381, B:K.518, B:K.518 pi-Stacking: B:F.288, B:F.288, B:Y.517, B:Y.517

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

EDO.2: 8 residues within 4Å: Chain A: L.53, G.57, Y.58, P.59, A.60, E.61, L.64, Y.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.57, A:A.60, A:E.61 EDO.5: 7 residues within 4Å: Chain B: L.53, G.57, Y.58, P.59, A.60, E.61, L.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.57, B:A.60, B:E.61

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

CL.3: 2 residues within 4Å: Chain A: S.181, K.187 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: S.181, K.187 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Structure of glutamine-dependent NAD+ synthetase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP). to be published

Release Date

2016-07-27

Peptides

Glutamine-dependent NAD+ synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamine-dependent NAD+ synthetase