SMTL ID : 1z0u.1

Crystal structure of a NAD kinase from Archaeoglobus fulgidus bound by NADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: S.63, E.64, K.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.64 Salt bridges: A:K.87 SO4.2: 4 residues within 4Å: Chain A: K.37, G.79, T.80, R.83 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.79 Water bridges: A:G.77, A:G.77 Salt bridges: A:K.37, A:R.83 SO4.4: 4 residues within 4Å: Chain B: K.37, G.79, T.80, R.83 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.79, B:T.80 Water bridges: B:G.77 Salt bridges: B:K.37, B:R.83 SO4.6: 3 residues within 4Å: Chain C: S.63, E.64, K.87 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.64 Salt bridges: C:K.87 SO4.7: 4 residues within 4Å: Chain C: K.37, G.79, T.80, R.83 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.79 Water bridges: C:G.77, C:G.77 Salt bridges: C:K.37, C:R.83 SO4.9: 4 residues within 4Å: Chain D: K.37, G.79, T.80, R.83 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.79, D:T.80 Water bridges: D:G.77 Salt bridges: D:K.37, D:R.83

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

NAP.3: 23 residues within 4Å: Chain A: G.77, D.78, G.79, L.82, R.83, R.101, L.104, N.144, E.145, I.182, T.185, G.186, Y.187, S.190, D.238, G.239, Q.240 Chain C: A.154, M.156, R.172, D.174, A.209, F.211 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:D.78, A:G.79, A:R.101, A:N.144, A:E.145, A:I.182, A:T.185, A:Y.187, A:S.190, A:S.190, A:D.238, A:Q.240, C:R.172, C:R.172 Water bridges: A:T.80, A:A.188, A:G.239, C:M.156 Salt bridges: A:R.83, A:R.83 pi-Stacking: A:Y.187 NAP.5: 23 residues within 4Å: Chain B: G.77, D.78, G.79, L.82, R.83, R.101, L.104, N.144, E.145, I.182, T.185, G.186, Y.187, S.190, D.238, G.239, Q.240 Chain D: A.154, M.156, R.172, D.174, A.209, F.211 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:D.78, B:G.79, B:R.101, B:N.144, B:N.144, B:E.145, B:Y.187, B:S.190, B:S.190, B:D.238, D:R.172, D:R.172 Water bridges: B:T.185, B:T.185, B:A.188 Salt bridges: B:R.83, B:R.83 pi-Stacking: B:Y.187 NAP.8: 23 residues within 4Å: Chain A: A.154, M.156, R.172, D.174, A.209, F.211 Chain C: G.77, D.78, G.79, L.82, R.83, R.101, L.104, N.144, E.145, I.182, T.185, G.186, Y.187, S.190, D.238, G.239, Q.240 21 PLIP interactions: 18 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:D.78, C:G.79, C:R.101, C:N.144, C:E.145, C:I.182, C:T.185, C:Y.187, C:S.190, C:S.190, C:D.238, C:Q.240, A:R.172, A:R.172 Water bridges: C:T.80, C:A.188, C:G.239, A:M.156 Salt bridges: C:R.83, C:R.83 pi-Stacking: C:Y.187 NAP.10: 23 residues within 4Å: Chain B: A.154, M.156, R.172, D.174, A.209, F.211 Chain D: G.77, D.78, G.79, L.82, R.83, R.101, L.104, N.144, E.145, I.182, T.185, G.186, Y.187, S.190, D.238, G.239, Q.240 18 PLIP interactions: 16 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:D.78, D:G.79, D:R.101, D:N.144, D:N.144, D:E.145, D:Y.187, D:S.190, D:S.190, D:D.238, B:R.172, B:R.172 Water bridges: D:T.185, D:T.185, D:A.188 Salt bridges: D:R.83, D:R.83 pi-Stacking: D:Y.187

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

2005-04-19

Peptides

Probable inorganic polyphosphate/ATP-NAD kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Probable inorganic polyphosphate/ATP-NAD kinase

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