SMTL ID : 5o6m.1

Structure of Polyphosphate Kinase from Meiothermus ruber N121D bound to ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

ATP.1: 13 residues within 4Å: Chain A: D.66, K.70, F.91, G.92, V.93, P.94, R.106, R.122, E.126, D.127, V.130, V.131, L.136 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.106, A:D.127 Water bridges: A:D.66, A:D.66, A:K.70, A:S.90, A:V.93, A:V.93, A:D.121, A:D.121, A:D.121, A:R.122, A:R.122 Salt bridges: A:K.70, A:R.122 ATP.9: 15 residues within 4Å: Chain B: D.66, K.70, D.71, F.91, G.92, V.93, P.94, R.106, R.122, E.126, D.127, V.130, V.131, L.136, R.193 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:R.106, B:E.126, B:D.127, B:R.193, B:R.193 Water bridges: B:K.70, B:K.70, B:V.93, B:R.122 Salt bridges: B:K.70, B:R.122, B:R.193, B:R.193, B:R.193 ATP.16: 15 residues within 4Å: Chain C: D.66, K.70, F.91, G.92, V.93, P.94, R.106, R.122, E.126, D.127, V.130, L.136, R.193, D.199 Ligands: PO4.17 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:V.93, C:R.106, C:E.126, C:D.127, C:R.193 Salt bridges: C:K.70, C:R.122 ATP.20: 14 residues within 4Å: Chain D: K.70, D.71, F.91, G.92, V.93, P.94, R.106, R.122, E.126, D.127, V.130, V.131, L.136, R.193 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:R.106, D:D.127 Water bridges: D:K.70, D:S.90, B:Y.51 Salt bridges: D:K.70, D:R.122, D:R.193, D:R.193

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

PO4.2: 6 residues within 4Å: Chain A: A.67, G.68, G.69, K.70, D.71, R.182 Ligand excluded by PLIP PO4.3: 3 residues within 4Å: Chain A: Q.97, R.101 Chain B: R.113 Ligand excluded by PLIP PO4.4: 3 residues within 4Å: Chain A: R.132, A.212, R.215 Ligand excluded by PLIP PO4.5: 4 residues within 4Å: Chain A: K.29, N.232, W.233 Ligands: PO4.7 Ligand excluded by PLIP PO4.6: 4 residues within 4Å: Chain A: R.182, K.188, K.191 Ligands: PO4.8 Ligand excluded by PLIP PO4.7: 3 residues within 4Å: Chain A: K.231, W.233 Ligands: PO4.5 Ligand excluded by PLIP PO4.8: 5 residues within 4Å: Chain A: G.72, R.75, N.232, R.235 Ligands: PO4.6 Ligand excluded by PLIP PO4.10: 6 residues within 4Å: Chain B: A.67, G.68, G.69, K.70, D.71, R.182 Ligand excluded by PLIP PO4.11: 3 residues within 4Å: Chain A: R.113 Chain B: Q.97, R.101 Ligand excluded by PLIP PO4.12: 5 residues within 4Å: Chain B: K.29, K.231, N.232, W.233 Ligands: PO4.14 Ligand excluded by PLIP PO4.13: 6 residues within 4Å: Chain B: G.69, G.72, R.75, N.232, R.235 Ligands: PO4.15 Ligand excluded by PLIP PO4.14: 3 residues within 4Å: Chain B: K.231, W.233 Ligands: PO4.12 Ligand excluded by PLIP PO4.15: 4 residues within 4Å: Chain B: R.182, K.188, K.191 Ligands: PO4.13 Ligand excluded by PLIP PO4.17: 7 residues within 4Å: Chain C: A.67, G.68, G.69, K.70, D.71, R.182 Ligands: ATP.16 Ligand excluded by PLIP PO4.18: 3 residues within 4Å: Chain C: Q.97, R.101 Chain D: R.113 Ligand excluded by PLIP PO4.19: 3 residues within 4Å: Chain C: K.29, N.232, W.233 Ligand excluded by PLIP PO4.21: 7 residues within 4Å: Chain D: A.67, G.68, G.69, K.70, D.71, R.182 Ligands: PO4.23 Ligand excluded by PLIP PO4.22: 3 residues within 4Å: Chain D: R.132, A.212, R.215 Ligand excluded by PLIP PO4.23: 6 residues within 4Å: Chain D: D.71, R.75, K.188, K.191 Ligands: PO4.21, PO4.25 Ligand excluded by PLIP PO4.24: 3 residues within 4Å: Chain D: K.29, N.232, W.233 Ligand excluded by PLIP PO4.25: 5 residues within 4Å: Chain D: G.72, R.75, N.232, R.235 Ligands: PO4.23 Ligand excluded by PLIP PO4.26: 3 residues within 4Å: Chain C: R.113 Chain D: Q.97, R.101 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parnell, A.E. et al., Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-03-21

Peptides

Polyphosphate:AMP phosphotransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Polyphosphate:AMP phosphotransferase

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