SMTL ID : 7qvs.1

Pseudomonas aeruginosa nicotinamide adenine dinucleotide kinase (NADK) structure in complex with NADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 2 residues within 4Å: Chain A: R.80, N.248 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.81, A:N.248 Salt bridges: A:R.80 PO4.3: 3 residues within 4Å: Chain B: R.80, R.84, N.248 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.248 Water bridges: B:A.81, B:R.84, B:R.84 Salt bridges: B:R.80, B:R.84 PO4.5: 2 residues within 4Å: Chain C: R.80, N.248 3 PLIP interactions: 3 interactions with chain C Water bridges: C:A.81, C:N.248 Salt bridges: C:R.80 PO4.7: 3 residues within 4Å: Chain D: R.80, R.84, N.248 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.248 Water bridges: D:A.81, D:R.84, D:R.84 Salt bridges: D:R.80, D:R.84

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 24 residues within 4Å: Chain A: R.12, G.71, D.72, G.73, L.76, R.94, F.99, N.146, D.147, T.184, T.187, A.188, Y.189, S.192, D.245, G.246, Q.247 Chain B: T.156, R.157, M.158, K.174, D.176, Y.211, H.213 29 PLIP interactions: 17 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:R.12, A:D.72, A:D.72, A:G.73, A:N.146, A:D.147, A:T.184, A:Y.189, A:S.192, A:D.245, A:Q.247, B:M.158, B:K.174, B:K.174, B:D.176, B:D.176 Water bridges: A:K.284, A:K.284, B:R.157, B:R.157, B:R.157, B:R.157, B:R.157 Salt bridges: A:R.12, A:R.94, A:K.284, B:R.157, B:R.157 pi-Stacking: A:Y.189 NAP.4: 20 residues within 4Å: Chain A: T.156, R.157, M.158, K.174, D.176, Y.211 Chain B: G.71, D.72, G.73, L.76, R.94, F.99, N.146, D.147, T.184, T.187, A.188, Y.189, S.192, D.245 18 PLIP interactions: 6 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:M.158, A:M.158, A:K.174, A:K.174, A:D.176, A:D.176, B:D.72, B:G.73, B:N.146, B:D.147, B:T.184, B:T.187, B:Y.189, B:S.192, B:D.245 Water bridges: B:D.147 Salt bridges: B:R.94 pi-Stacking: B:Y.189 NAP.6: 24 residues within 4Å: Chain C: R.12, G.71, D.72, G.73, L.76, R.94, F.99, N.146, D.147, T.184, T.187, A.188, Y.189, S.192, D.245, G.246, Q.247 Chain D: T.156, R.157, M.158, K.174, D.176, Y.211, H.213 29 PLIP interactions: 17 interactions with chain C, 12 interactions with chain D Hydrogen bonds: C:R.12, C:D.72, C:G.73, C:N.146, C:D.147, C:T.184, C:T.187, C:Y.189, C:S.192, C:D.245, C:Q.247, D:M.158, D:K.174, D:K.174, D:D.176, D:D.176 Water bridges: C:K.284, C:K.284, D:R.157, D:R.157, D:R.157, D:R.157, D:R.157 Salt bridges: C:R.12, C:R.94, C:K.284, D:R.157, D:R.157 pi-Stacking: C:Y.189 NAP.8: 20 residues within 4Å: Chain C: T.156, R.157, M.158, K.174, D.176, Y.211 Chain D: G.71, D.72, G.73, L.76, R.94, F.99, N.146, D.147, T.184, T.187, A.188, Y.189, S.192, D.245 18 PLIP interactions: 11 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:D.72, D:G.73, D:N.146, D:D.147, D:T.184, D:Y.189, D:S.192, D:D.245, C:M.158, C:M.158, C:K.174, C:K.174, C:D.176, C:D.176 Water bridges: D:A.190, C:T.156 Salt bridges: D:R.94 pi-Stacking: D:Y.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rahimova, R. et al., Structure-based design, synthesis and biological evaluation of a NAD + analogue targeting Pseudomonas aeruginosa NAD kinase. Febs J. (2023)

Release Date

2022-09-14

Peptides

NAD kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

NAD kinase