SMTL ID : 6rbw.1

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complexe with an adenine derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

CIT.1: 8 residues within 4Å: Chain A: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.98 Hydrogen bonds: A:Y.100, A:F.251, A:F.253 Salt bridges: A:H.173, A:H.173, A:R.247, A:R.256 CIT.3: 8 residues within 4Å: Chain B: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.98 Hydrogen bonds: B:Y.100, B:F.251, B:F.253 Salt bridges: B:H.173, B:H.173, B:R.247, B:R.256 CIT.5: 8 residues within 4Å: Chain C: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.98 Hydrogen bonds: C:F.251, C:F.253 Salt bridges: C:H.173, C:H.173, C:R.247, C:R.256 CIT.7: 8 residues within 4Å: Chain D: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.98 Hydrogen bonds: D:F.251, D:F.253 Salt bridges: D:H.173, D:H.173, D:R.247, D:R.256

4 x JXB: 9-(4-azidobutyl)-8-bromanyl-purin-6-amine(Non-covalent)

JXB.2: 12 residues within 4Å: Chain A: D.45, G.46, L.49, F.74, Y.75, N.122, S.158, T.161, A.162, Y.163, S.166 Chain D: I.187 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.122, A:S.158, A:T.161, A:S.166, A:S.166 Water bridges: A:Y.163 JXB.4: 12 residues within 4Å: Chain B: D.45, G.46, L.49, F.74, Y.75, N.122, S.158, T.161, A.162, Y.163, S.166 Chain C: I.187 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.122, B:S.158, B:T.161, B:S.166 Water bridges: B:Y.163 JXB.6: 12 residues within 4Å: Chain B: I.187 Chain C: D.45, G.46, L.49, F.74, Y.75, N.122, S.158, T.161, A.162, Y.163, S.166 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.75, C:N.122, C:S.158, C:S.166, C:S.166 Water bridges: C:Y.163 JXB.8: 12 residues within 4Å: Chain A: I.187 Chain D: D.45, G.46, L.49, F.74, Y.75, N.122, S.158, T.161, A.162, Y.163, S.166 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.75, D:N.122, D:S.158, D:S.166 Water bridges: D:Y.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gelin, M. et al., From Substrate to Fragments to Inhibitor ActiveIn VivoagainstStaphylococcus aureus. Acs Infect Dis. (2020)

Release Date

2020-02-19

Peptides

NAD kinase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

NAD kinase 1

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