SMTL ID : 6z61.1

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a di-adenosine derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.47 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 Q9H: (2~{R},3~{R},4~{S},5~{R})-2-[6-azanyl-8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-[6-(2-azanylethylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]prop-1-ynyl]purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol(Non-covalent)

Q9H.2: 17 residues within 4Å: Chain A: D.45, G.46, L.49, H.71, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, D.222, H.223 Chain D: D.150, I.187, Y.192 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.49 Hydrogen bonds: A:D.45, A:N.122, A:S.158, A:T.161, A:Y.163, A:D.222, D:D.150 Q9H.4: 17 residues within 4Å: Chain B: D.45, G.46, L.49, H.71, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, D.222, H.223 Chain C: D.150, I.187, Y.192 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain B Hydrogen bonds: C:D.150, B:D.45, B:N.122, B:S.158, B:T.161, B:Y.163, B:D.222 Hydrophobic interactions: B:L.49 Q9H.6: 17 residues within 4Å: Chain B: D.150, I.187, Y.192 Chain C: D.45, G.46, L.49, H.71, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, D.222, H.223 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.49 Hydrogen bonds: C:D.45, C:D.45, C:Y.75, C:N.122, C:S.158, C:Y.163, C:D.222, B:D.150 Q9H.8: 17 residues within 4Å: Chain A: D.150, I.187, Y.192 Chain D: D.45, G.46, L.49, H.71, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, D.222, H.223 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain D Hydrogen bonds: A:D.150, D:D.45, D:D.45, D:Y.75, D:N.122, D:S.158, D:Y.163, D:D.222 Hydrophobic interactions: D:L.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clement, D.A. et al., New Chemical Probe Targeting Bacterial NAD Kinase. Molecules (2020)

Release Date

2021-05-26

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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