SMTL ID : 5o6k.1

Structure of Polyphosphate Kinase from Meiothermus ruber N121D

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: D.66, A.67, G.68, G.69, K.70, D.71, R.182 Ligands: PO4.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.66, A:A.67, A:G.68, A:G.69, A:K.70, A:D.71, A:R.182 Salt bridges: A:K.70 PO4.2: 3 residues within 4Å: Chain A: K.231, W.233 Ligands: PO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.233 Salt bridges: A:K.231 PO4.3: 5 residues within 4Å: Chain A: K.29, K.231, N.232, W.233 Ligands: PO4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.232, A:W.233, A:W.233 PO4.4: 6 residues within 4Å: Chain A: D.71, G.72, R.75, K.188, K.191 Ligands: PO4.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.72 Salt bridges: A:R.75, A:K.191 PO4.5: 6 residues within 4Å: Chain B: D.66, A.67, G.68, G.69, K.70, D.71 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.66, B:A.67, B:G.68, B:G.69, B:K.70, B:D.71 Salt bridges: B:K.70 PO4.8: 7 residues within 4Å: Chain C: D.66, A.67, G.68, G.69, K.70, D.71, R.182 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.66, C:A.67, C:G.69, C:K.70, C:D.71 Salt bridges: C:K.70, C:R.182 PO4.9: 3 residues within 4Å: Chain C: K.29, N.232, W.233 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.232, C:N.232, C:N.232, C:W.233 Salt bridges: C:K.29 PO4.10: 8 residues within 4Å: Chain D: D.66, A.67, G.68, G.69, K.70, D.71, R.182 Ligands: PO4.12 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:D.66, D:A.67, D:G.68, D:G.69, D:K.70, D:D.71 Salt bridges: D:K.70, D:R.182 PO4.11: 3 residues within 4Å: Chain D: K.29, N.232, W.233 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.233 Salt bridges: D:K.29 PO4.12: 5 residues within 4Å: Chain D: R.75, R.182, K.188, K.191 Ligands: PO4.10 3 PLIP interactions: 3 interactions with chain D Salt bridges: D:R.75, D:R.182, D:K.191

2 x DPO: DIPHOSPHATE(Non-covalent)

DPO.6: 3 residues within 4Å: Chain B: K.231, W.233 Ligands: DPO.7 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.231, B:K.231 DPO.7: 6 residues within 4Å: Chain B: K.29, N.230, K.231, N.232, W.233 Ligands: DPO.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.232, B:W.233 Salt bridges: B:K.29

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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