SMTL ID : 6rc6.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-tetramer

Ligands

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

CIT.1: 9 residues within 4Å: Chain A: V.98, Y.100, H.173, R.247, R.249, F.251, P.252, F.253, R.256 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.98 Hydrogen bonds: A:Y.100, A:R.249, A:F.251, A:F.253 Water bridges: A:W.254 Salt bridges: A:H.173, A:H.173, A:R.247, A:R.256 CIT.3: 9 residues within 4Å: Chain B: V.98, Y.100, H.173, R.247, R.249, F.251, P.252, F.253, R.256 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.98 Hydrogen bonds: B:Y.100, B:R.249, B:F.251, B:F.253 Water bridges: B:W.254 Salt bridges: B:H.173, B:H.173, B:R.247, B:R.256 CIT.5: 9 residues within 4Å: Chain C: V.98, Y.100, H.173, R.247, R.249, F.251, P.252, F.253, R.256 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.98 Hydrogen bonds: C:R.249, C:F.251, C:F.253 Water bridges: C:W.254 Salt bridges: C:H.173, C:H.173, C:R.247, C:R.256 CIT.7: 9 residues within 4Å: Chain D: V.98, Y.100, H.173, R.247, R.249, F.251, P.252, F.253, R.256 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:V.98 Hydrogen bonds: D:R.249, D:F.251, D:F.253 Water bridges: D:W.254 Salt bridges: D:H.173, D:H.173, D:R.247, D:R.256

4 x JY5: 3-[6-azanyl-9-[(2~{R})-oxan-2-yl]purin-8-yl]prop-2-yn-1-ol(Non-covalent)

JY5.2: 10 residues within 4Å: Chain A: D.45, G.46, L.49, F.74, Y.75, N.122, S.158, T.161, A.162, H.223 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.45, A:L.49 Hydrogen bonds: A:N.122, A:S.158, A:T.161 JY5.4: 10 residues within 4Å: Chain B: D.45, G.46, L.49, F.74, Y.75, N.122, S.158, T.161, A.162, H.223 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:D.45, B:L.49 Hydrogen bonds: B:N.122, B:S.158, B:T.161 JY5.6: 10 residues within 4Å: Chain C: D.45, G.46, L.49, F.74, Y.75, N.122, S.158, T.161, A.162, H.223 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:D.45, C:L.49 Hydrogen bonds: C:D.45, C:N.122, C:S.158 Water bridges: C:T.161, C:T.161 JY5.8: 10 residues within 4Å: Chain D: D.45, G.46, L.49, F.74, Y.75, N.122, S.158, T.161, A.162, H.223 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:D.45, D:L.49 Hydrogen bonds: D:D.45, D:N.122, D:S.158 Water bridges: D:T.161, D:T.161

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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