SMTL ID : 1z0s.1

Crystal structure of an NAD kinase from Archaeoglobus fulgidus in complex with ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 2 residues within 4Å: Ligands: ATP.2, POP.3 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Ligands: ATP.5, POP.6 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Ligands: ATP.8, POP.9 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Ligands: ATP.11, POP.12 No protein-ligand interaction detected (PLIP)

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 20 residues within 4Å: Chain A: G.79, L.82, R.83, N.144, E.145, G.186, Y.187, S.190, D.238, G.239, Q.240 Chain D: A.154, K.155, M.156, R.172, D.174, A.209, F.211 Ligands: MG.1, POP.3 18 PLIP interactions: 6 interactions with chain D, 12 interactions with chain A Hydrogen bonds: D:R.172, A:N.144, A:E.145, A:Y.187, A:S.190, A:S.190, A:D.238, A:Q.240 Water bridges: D:M.156, A:R.101, A:E.145 Salt bridges: D:K.155, D:K.155, D:K.155, A:R.83, A:R.83 pi-Stacking: D:F.211, A:Y.187 ATP.5: 20 residues within 4Å: Chain B: G.79, L.82, R.83, N.144, E.145, G.186, Y.187, S.190, D.238, G.239, Q.240 Chain C: A.154, K.155, M.156, R.172, D.174, A.209, F.211 Ligands: MG.4, POP.6 20 PLIP interactions: 12 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:N.144, B:E.145, B:Y.187, B:S.190, B:S.190, B:D.238, B:Q.240, C:R.172 Water bridges: B:A.188, C:K.155, C:K.155, C:M.156 Salt bridges: B:K.37, B:R.83, B:R.83, C:K.155, C:K.155, C:K.155 pi-Stacking: B:Y.187, C:F.211 ATP.8: 20 residues within 4Å: Chain B: A.154, K.155, M.156, R.172, D.174, A.209, F.211 Chain C: G.79, L.82, R.83, N.144, E.145, G.186, Y.187, S.190, D.238, G.239, Q.240 Ligands: MG.7, POP.9 18 PLIP interactions: 12 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:G.79, C:N.144, C:E.145, C:Y.187, C:S.190, C:S.190, C:D.238, C:Q.240, B:R.172 Water bridges: C:A.188, B:M.156, B:M.156 Salt bridges: C:R.83, C:R.83, B:K.155, B:K.155, B:K.155 pi-Stacking: C:Y.187 ATP.11: 20 residues within 4Å: Chain A: A.154, K.155, M.156, R.172, D.174, A.209, F.211 Chain D: G.79, L.82, R.83, N.144, E.145, G.186, Y.187, S.190, D.238, G.239, Q.240 Ligands: MG.10, POP.12 19 PLIP interactions: 11 interactions with chain D, 8 interactions with chain A Hydrogen bonds: D:N.144, D:E.145, D:Y.187, D:S.190, D:S.190, D:D.238, D:Q.240, A:R.172 Water bridges: D:A.188, A:K.155, A:M.156, A:M.156, A:M.156 Salt bridges: D:R.83, D:R.83, A:K.155, A:K.155, A:K.155 pi-Stacking: D:Y.187

4 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.3: 11 residues within 4Å: Chain A: K.37, G.76, G.77, D.78, G.79, T.80, R.83, G.100, R.101 Ligands: MG.1, ATP.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.77, A:D.78, A:G.79, A:T.80, A:R.101 Water bridges: A:T.99, A:R.101 Salt bridges: A:K.37, A:K.37, A:R.83, A:R.101 POP.6: 10 residues within 4Å: Chain B: K.37, G.76, G.77, D.78, G.79, T.80, R.83, R.101 Ligands: MG.4, ATP.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.77, B:G.77, B:D.78, B:G.79, B:T.80, B:R.101 Water bridges: B:V.102 Salt bridges: B:K.37, B:R.83, B:R.101 POP.9: 9 residues within 4Å: Chain C: K.37, G.77, D.78, G.79, T.80, R.83, R.101 Ligands: MG.7, ATP.8 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.77, C:G.77, C:D.78, C:G.79, C:T.80, C:T.80, C:R.101 Water bridges: C:V.102 Salt bridges: C:K.37, C:K.37, C:R.83 POP.12: 10 residues within 4Å: Chain D: K.37, G.76, G.77, G.79, T.80, R.83, G.100, R.101 Ligands: MG.10, ATP.11 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.77, D:G.79, D:T.80, D:T.80, D:R.101 Salt bridges: D:K.37, D:K.37, D:R.83, D:R.101

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
C

D
D

Probable inorganic polyphosphate/ATP-NAD kinase

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