SMTL ID : 5lcd.1

Structure of Polyphosphate Kinase from Meiothermus ruber bound to AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

homo-tetramer

Ligands

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 11 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, L.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.126, A:D.147 AMP.7: 11 residues within 4Å: Chain B: F.111, G.112, V.113, P.114, R.126, R.142, E.146, D.147, V.150, V.151, L.156 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.126, B:D.147 Water bridges: B:E.146 AMP.12: 13 residues within 4Å: Chain C: F.111, G.112, V.113, P.114, R.126, R.142, E.146, D.147, V.150, V.151, L.156, R.213 Ligands: MG.13 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.126, C:E.146, C:D.147 Salt bridges: C:R.213 AMP.17: 11 residues within 4Å: Chain D: F.111, G.112, V.113, P.114, R.126, R.142, E.146, D.147, V.150, V.151, L.156 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.126, D:D.147 Salt bridges: D:R.142

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

PO4.2: 9 residues within 4Å: Chain A: M.85, D.86, A.87, G.88, G.89, K.90, D.91, R.202 Ligands: SO4.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:A.87, A:A.87, A:G.88, A:G.89, A:K.90, A:D.91 Salt bridges: A:K.90, A:R.202, A:K.211 PO4.8: 8 residues within 4Å: Chain B: M.85, A.87, G.88, G.89, K.90, D.91, R.202 Ligands: SO4.9 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:M.85, B:A.87, B:G.88, B:G.89, B:K.90, B:D.91 Salt bridges: B:K.90, B:R.202, B:K.211 PO4.14: 9 residues within 4Å: Chain C: M.85, D.86, A.87, G.88, G.89, K.90, D.91, R.202 Ligands: SO4.15 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:A.87, C:G.88, C:G.89, C:K.90, C:D.91 Salt bridges: C:K.90, C:R.202 PO4.18: 8 residues within 4Å: Chain D: M.85, D.86, A.87, G.88, G.89, K.90, D.91, R.202 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.86, D:A.87, D:G.88, D:G.89, D:K.90, D:D.91 Salt bridges: D:K.90

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: Q.117, R.121 Chain B: R.133 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A Water bridges: C:S.110 Salt bridges: B:R.133, A:R.121 Hydrogen bonds: A:Q.117 SO4.4: 4 residues within 4Å: Chain A: K.49, K.251, N.252, W.253 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.252, A:N.252, A:W.253 Salt bridges: A:K.49 SO4.5: 2 residues within 4Å: Chain A: K.251, W.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.253 Salt bridges: A:K.251 SO4.6: 7 residues within 4Å: Chain A: D.91, G.92, R.95, R.202, K.208, K.211 Ligands: PO4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.92 Salt bridges: A:R.95, A:R.202, A:K.208, A:K.211 SO4.9: 6 residues within 4Å: Chain B: D.91, G.92, R.95, K.208, K.211 Ligands: PO4.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.92 Salt bridges: B:R.95, B:K.208, B:K.211 SO4.10: 3 residues within 4Å: Chain B: K.251, W.253 Ligands: SO4.11 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.251 SO4.11: 5 residues within 4Å: Chain B: K.49, K.251, N.252, W.253 Ligands: SO4.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.252, B:N.252, B:W.253 Salt bridges: B:K.49 SO4.15: 6 residues within 4Å: Chain C: D.91, R.95, R.202, K.208, K.211 Ligands: PO4.14 4 PLIP interactions: 4 interactions with chain C Salt bridges: C:R.95, C:R.202, C:K.208, C:K.211 SO4.16: 3 residues within 4Å: Chain C: R.152, A.232, R.235 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.152, C:R.235 SO4.19: 3 residues within 4Å: Chain C: R.133 Chain D: Q.117, R.121 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.117 Salt bridges: D:R.121, C:R.133

1 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 2 residues within 4Å: Chain C: R.142 Ligands: AMP.12 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: AMP.12

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

2017-06-21

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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