SMTL ID : 2i29.1

Crystal structure of NAD kinase 1 from Listeria monocytogenes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 18 residues within 4Å: Chain A: D.45, G.46, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222, H.223 Chain D: G.149, D.150, A.185, I.187, Y.192 11 PLIP interactions: 1 interactions with chain D, 10 interactions with chain A Hydrogen bonds: D:D.150, A:N.122, A:E.123, A:S.158, A:T.161, A:Y.163, A:S.166, A:D.222 Water bridges: A:D.45, A:D.45 pi-Stacking: A:Y.163 NAD.3: 18 residues within 4Å: Chain B: D.45, G.46, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222, H.223 Chain C: G.149, D.150, A.185, I.187, Y.192 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.122, B:E.123, B:S.158, B:T.161, B:Y.163, B:S.166, B:D.222, C:D.150 Water bridges: B:D.45, B:D.45 pi-Stacking: B:Y.163 NAD.5: 18 residues within 4Å: Chain B: G.149, D.150, A.185, I.187, Y.192 Chain C: D.45, G.46, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222, H.223 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.45, C:N.122, C:E.123, C:S.158, C:Y.163, C:S.166, C:D.222, B:D.150 Water bridges: C:D.45, C:D.45 pi-Stacking: C:Y.163 NAD.7: 18 residues within 4Å: Chain A: G.149, D.150, A.185, I.187, Y.192 Chain D: D.45, G.46, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222, H.223 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:D.45, D:N.122, D:E.123, D:S.158, D:Y.163, D:S.166, D:D.222, A:D.150 Water bridges: D:D.45, D:D.45 pi-Stacking: D:Y.163

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

CIT.2: 7 residues within 4Å: Chain A: Y.100, H.173, R.247, F.251, P.252, F.253 Chain C: H.205 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain A Salt bridges: C:H.205, A:H.173, A:H.173, A:R.247 Hydrogen bonds: A:Y.100, A:F.253 Water bridges: A:R.256 CIT.4: 7 residues within 4Å: Chain B: Y.100, H.173, R.247, F.251, P.252, F.253 Chain D: H.205 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Y.100, B:F.253 Water bridges: B:R.256 Salt bridges: B:H.173, B:H.173, B:R.247, D:H.205 CIT.6: 7 residues within 4Å: Chain A: H.205 Chain C: Y.100, H.173, R.247, F.251, P.252, F.253 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain C Salt bridges: A:H.205, C:H.173, C:H.173, C:R.247 Hydrogen bonds: C:F.253 Water bridges: C:Y.100, C:R.256 CIT.8: 7 residues within 4Å: Chain B: H.205 Chain D: Y.100, H.173, R.247, F.251, P.252, F.253 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:F.253 Water bridges: D:Y.100, D:R.256 Salt bridges: D:H.173, D:H.173, D:R.247, B:H.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Poncet-Montange, G. et al., NAD kinases use substrate-assisted catalysis for specific recognition of NAD. J.Biol.Chem. (2007)

Release Date

2007-08-07

Peptides

Probable inorganic polyphosphate/ATP-NAD kinase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Probable inorganic polyphosphate/ATP-NAD kinase 1

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