SMTL ID : 1suw.1

Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with its substrate and product: Insights into the catalysis of NAD kinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 24 residues within 4Å: Chain A: G.48, D.49, G.50, L.53, R.54, V.73, L.75, N.115, E.116, I.153, T.156, G.157, Y.158, S.161, D.209, G.210, Q.211 Chain D: A.125, K.126, M.127, R.143, D.145, A.180, F.182 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:D.49, A:D.49, A:G.50, A:N.115, A:E.116, A:I.153, A:T.156, A:Y.158, A:S.161, A:S.161, A:D.209, A:Q.211, D:R.143, D:R.143 Water bridges: A:A.159, D:A.125 Salt bridges: A:R.54, A:R.54, D:K.126 pi-Stacking: A:Y.158 NAP.2: 23 residues within 4Å: Chain B: G.48, D.49, G.50, L.53, R.54, V.73, L.75, N.115, E.116, I.153, T.156, G.157, Y.158, S.161, D.209, G.210, Q.211 Chain C: A.125, M.127, R.143, D.145, A.180, F.182 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:D.49, B:G.50, B:V.73, B:N.115, B:E.116, B:I.153, B:Y.158, B:S.161, B:S.161, C:R.143, C:R.143 Water bridges: B:D.49, B:D.49, B:T.51, B:T.51, B:A.159, B:G.210 Salt bridges: B:R.54, B:R.54 pi-Stacking: B:Y.158 NAP.3: 24 residues within 4Å: Chain B: A.125, K.126, M.127, R.143, D.145, A.180, F.182 Chain C: G.48, D.49, G.50, L.53, R.54, V.73, L.75, N.115, E.116, I.153, T.156, G.157, Y.158, S.161, D.209, G.210, Q.211 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:D.49, C:D.49, C:G.50, C:N.115, C:E.116, C:I.153, C:Y.158, C:S.161, C:S.161, C:D.209, C:Q.211, B:R.143, B:R.143 Water bridges: C:T.156, C:T.156, C:A.159 Salt bridges: C:R.54, C:R.54, B:K.126 pi-Stacking: C:Y.158 NAP.4: 23 residues within 4Å: Chain A: A.125, M.127, R.143, D.145, A.180, F.182 Chain D: G.48, D.49, G.50, L.53, R.54, V.73, L.75, N.115, E.116, I.153, T.156, G.157, Y.158, S.161, D.209, G.210, Q.211 22 PLIP interactions: 18 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:D.49, D:G.50, D:N.115, D:N.115, D:E.116, D:T.156, D:Y.158, D:S.161, D:D.209, D:Q.211, A:R.143, A:R.143, A:A.180 Water bridges: D:T.51, D:V.73, D:V.73, D:A.159, D:G.210, A:A.125 Salt bridges: D:R.54, D:R.54 pi-Stacking: D:Y.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., Crystal Structures of an NAD Kinase from Archaeoglobus fulgidus in Complex with ATP, NAD, or NADP. J.Mol.Biol. (2005)

Release Date

2004-08-24

Peptides

Probable inorganic polyphosphate/ATP-NAD kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Probable inorganic polyphosphate/ATP-NAD kinase