SMTL ID : 4dy6.1

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 2'-phosphate bis(adenosine)-5'-diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x A22: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE(Non-covalent)

A22.1: 19 residues within 4Å: Chain A: G.44, D.45, G.46, H.71, 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 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:D.45, A:G.46, A:N.122, A:E.123, A:S.158, A:T.161, A:Y.163, A:S.166, D:A.185 Water bridges: A:T.47, A:H.223, A:H.223 Salt bridges: A:H.71, A:H.223 pi-Stacking: A:Y.163, A:Y.163 A22.3: 19 residues within 4Å: Chain B: G.44, D.45, G.46, H.71, 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 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.45, B:G.46, B:N.122, B:E.123, B:S.158, B:T.161, B:Y.163, B:S.166, C:A.185 Water bridges: B:T.47, B:H.223, B:H.223 Salt bridges: B:H.71, B:H.223 pi-Stacking: B:Y.163, B:Y.163 A22.5: 19 residues within 4Å: Chain B: G.149, D.150, A.185, I.187 Chain C: G.44, D.45, G.46, H.71, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222, H.223 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.45, C:D.45, C:G.46, C:Y.75, C:N.122, C:E.123, C:S.158, C:Y.163, C:S.166, B:A.185 Water bridges: C:T.47, C:T.161 Salt bridges: C:H.71, C:H.223 pi-Stacking: C:Y.163, C:Y.163 A22.7: 19 residues within 4Å: Chain A: G.149, D.150, A.185, I.187 Chain D: G.44, D.45, G.46, H.71, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222, H.223 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:D.45, D:D.45, D:G.46, D:Y.75, D:N.122, D:E.123, D:S.158, D:Y.163, D:S.166, A:A.185 Water bridges: D:T.47, D:T.161 Salt bridges: D:H.71, D:H.223 pi-Stacking: D:Y.163, D:Y.163

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

CIT.2: 8 residues within 4Å: Chain A: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.98 Hydrogen bonds: A:Y.100, A:R.247, A:F.253, A:R.256 Salt bridges: A:H.173, A:H.173, A:R.247, A:R.256 CIT.4: 8 residues within 4Å: Chain B: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.98 Hydrogen bonds: B:Y.100, B:R.247, B:F.253, B:R.256 Salt bridges: B:H.173, B:H.173, B:R.247, B:R.256 CIT.6: 8 residues within 4Å: Chain C: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.98 Hydrogen bonds: C:R.247, C:F.253, C:R.256 Salt bridges: C:H.173, C:H.173, C:R.247, C:R.256 CIT.8: 8 residues within 4Å: Chain D: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.98 Hydrogen bonds: D:R.247, D:F.253, D:R.256 Salt bridges: D:H.173, D:H.173, D:R.247, D:R.256

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

2012-03-07

Peptides

inorganic polyphosphate/ATP-NAD kinase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

inorganic polyphosphate/ATP-NAD kinase 1

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