SMTL ID : 5maq.1

Crystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ADP and PPi

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-tetramer

Ligands

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 12 residues within 4Å: Chain A: F.111, G.112, V.113, P.114, R.126, R.142, E.146, D.147, V.150, V.151 Ligands: PPV.2, MG.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.126, A:D.147 Water bridges: A:E.146 Salt bridges: A:K.90, A:R.142 ADP.4: 15 residues within 4Å: Chain B: D.86, F.111, G.112, V.113, P.114, R.126, R.142, E.146, D.147, V.150, V.151, L.156 Ligands: PPV.5, MG.6, MG.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.126, B:D.147 Salt bridges: B:R.142 ADP.8: 12 residues within 4Å: Chain C: D.86, F.111, G.112, V.113, P.114, R.126, R.142, E.146, D.147, V.150, V.151 Ligands: PPV.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.86, C:R.126, C:D.147 Salt bridges: C:R.142, C:R.213 ADP.10: 14 residues within 4Å: Chain D: D.86, F.111, G.112, V.113, P.114, R.126, R.142, E.146, D.147, V.150, V.151, L.156 Ligands: PPV.11, MG.12 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.86, D:R.126, D:D.147 Salt bridges: D:R.142

4 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.2: 10 residues within 4Å: Chain A: M.85, D.86, A.87, G.88, G.89, K.90, D.91, R.202 Ligands: ADP.1, MG.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:A.87, A:G.88, A:G.89, A:K.90, A:D.91 Water bridges: A:G.92 Salt bridges: A:K.90, A:K.90, A:R.202 PPV.5: 12 residues within 4Å: Chain B: M.85, D.86, A.87, G.88, G.89, K.90, D.91, R.142, R.202, K.211 Ligands: ADP.4, MG.6 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:D.86, B:A.87, B:G.88, B:G.89, B:K.90, B:D.91, B:D.91, B:R.142 Salt bridges: B:K.90, B:K.90, B:R.202, B:K.211, B:K.211 PPV.9: 10 residues within 4Å: Chain C: M.85, D.86, A.87, G.88, G.89, K.90, D.91, R.202, K.211 Ligands: ADP.8 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:M.85, C:D.86, C:A.87, C:G.88, C:G.89, C:K.90, C:D.91 Salt bridges: C:K.90, C:K.90, C:R.202, C:K.211, C:K.211 PPV.11: 11 residues within 4Å: Chain D: M.85, D.86, A.87, G.88, G.89, K.90, D.91, R.142, R.202 Ligands: ADP.10, MG.12 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:D.86, D:A.87, D:G.88, D:G.89, D:K.90, D:D.91, D:R.142 Salt bridges: D:K.90, D:K.90, D:R.202

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: K.211 Ligands: ADP.1, PPV.2 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: K.211 Ligands: ADP.4, PPV.5 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: D.86, D.216 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.86 MG.12: 3 residues within 4Å: Chain D: K.211 Ligands: ADP.10, PPV.11 No protein-ligand interaction detected (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

2017-12-20

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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