SMTL ID : 1xdp.2 (1 other biounit)

Crystal Structure of the E.coli Polyphosphate Kinase in complex with AMPPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: R.374, R.404 Ligands: MG.2, ATP.5 No protein-ligand interaction detected (PLIP) MG.2: 5 residues within 4Å: Chain A: Y.373, R.374, R.404 Ligands: MG.1, ATP.5 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain B: R.404 Ligands: MG.4, ATP.6 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: R.52, R.404 Ligands: MG.3, ATP.6 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain C: R.374, R.404 Ligands: MG.8, ATP.11 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain C: Y.373, R.374, R.404 Ligands: MG.7, ATP.11 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain D: R.404 Ligands: MG.10, ATP.12 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain D: R.52, R.404 Ligands: MG.9, ATP.12 No protein-ligand interaction detected (PLIP)

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

ATP.5: 15 residues within 4Å: Chain A: F.16, V.20, I.40, N.44, Y.373, R.374, R.404, H.434, Y.467, R.563, L.589, H.591, R.593 Ligands: MG.1, MG.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.44, A:R.52, A:Y.373, A:R.404, A:N.458, A:Y.467, A:Y.467, A:R.593 Water bridges: A:N.537, A:N.537, A:R.563, A:R.563 Salt bridges: A:R.374, A:R.374, A:H.434, A:R.563, A:H.591, A:H.591, A:H.591 ATP.6: 16 residues within 4Å: Chain B: F.16, V.20, I.40, N.44, Y.373, R.374, R.404, H.434, Y.467, R.563, D.586, L.589, H.591, R.593 Ligands: MG.3, MG.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:N.44, B:Y.373, B:R.404, B:N.458, B:Y.467, B:Y.467, B:R.593, B:R.593 Salt bridges: B:R.374, B:R.374, B:H.434, B:R.563, B:H.591, B:H.591 ATP.11: 15 residues within 4Å: Chain C: F.16, V.20, I.40, N.44, Y.373, R.374, R.404, H.434, Y.467, R.563, L.589, H.591, R.593 Ligands: MG.7, MG.8 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:N.44, C:R.52, C:Y.373, C:R.404, C:N.458, C:Y.467, C:Y.467, C:R.593 Water bridges: C:N.537, C:N.537, C:R.563, C:R.563 Salt bridges: C:R.374, C:R.374, C:H.434, C:R.563, C:H.591, C:H.591, C:H.591 ATP.12: 16 residues within 4Å: Chain D: F.16, V.20, I.40, N.44, Y.373, R.374, R.404, H.434, Y.467, R.563, D.586, L.589, H.591, R.593 Ligands: MG.9, MG.10 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:N.44, D:Y.373, D:R.404, D:N.458, D:Y.467, D:Y.467, D:R.593, D:R.593 Salt bridges: D:R.374, D:R.374, D:H.434, D:R.563, D:H.591, D:H.591

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, Y. et al., Crystal structure of a polyphosphate kinase and its implications for polyphosphate synthesis. Embo Rep. (2005)

Release Date

2005-06-21

Peptides

Polyphosphate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Polyphosphate kinase

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