SMTL ID : 5ld1.1

Crystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-tetramer

Ligands

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

ATP.1: 17 residues within 4Å: Chain A: A.84, D.86, K.90, 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: ATP.2, MG.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:A.84, A:D.86, A:R.126, A:D.147, A:R.213 Water bridges: A:V.113, A:V.113, A:E.146, A:D.147, A:D.147, A:R.202, A:R.213 Salt bridges: A:K.90, A:R.142, A:R.142, A:R.142, A:R.213, A:R.213 ATP.2: 20 residues within 4Å: Chain A: M.85, D.86, A.87, G.88, G.89, K.90, D.91, N.141, R.142, R.202, W.210, K.211 Chain D: Q.67, E.68, Y.71, N.102, S.104, G.105 Ligands: ATP.1, MG.3 31 PLIP interactions: 25 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:M.85, A:D.86, A:A.87, A:A.87, A:G.88, A:G.89, A:K.90, A:D.91, A:N.141, A:N.141, A:N.141, A:R.142, A:R.202, D:Q.67, D:Q.67, D:N.102, D:S.104 Water bridges: A:G.92, A:S.110, A:S.110, A:R.142, A:R.198, A:R.202, A:K.211, D:N.102 Salt bridges: A:K.90, A:K.90, A:R.142, A:R.202, A:K.211 pi-Stacking: D:Y.71 ATP.5: 18 residues within 4Å: Chain B: A.84, D.86, K.90, F.111, G.112, V.113, P.114, R.126, R.142, E.146, D.147, V.150, V.151, L.156 Ligands: ATP.6, MG.7, GOL.8, MG.10 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:A.84, B:D.86, B:R.126, B:D.147 Water bridges: B:R.142, B:R.202, C:Y.71 Salt bridges: B:K.90, B:R.142, B:R.142, B:R.142 ATP.6: 20 residues within 4Å: Chain B: M.85, D.86, A.87, G.88, G.89, K.90, D.91, N.141, R.142, R.202, W.210, K.211 Chain C: Q.67, E.68, Y.71, N.102, S.104, G.105 Ligands: ATP.5, MG.7 34 PLIP interactions: 23 interactions with chain B, 11 interactions with chain C Hydrogen bonds: B:M.85, B:A.87, B:G.88, B:G.89, B:K.90, B:D.91, B:N.141, B:R.142, B:R.142, B:R.202, C:Q.67, C:Q.67, C:Y.71, C:N.102, C:S.104 Water bridges: B:D.91, B:G.92, B:S.110, B:S.110, B:R.198, B:R.202, B:K.211, B:K.211, C:E.68, C:E.68, C:E.68, C:N.102, C:S.104 Salt bridges: B:K.90, B:K.90, B:R.142, B:R.202, B:K.211 pi-Stacking: C:Y.71 ATP.12: 18 residues within 4Å: Chain C: A.84, D.86, K.90, 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: ATP.13, MG.14, GOL.15 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:A.84, C:D.86, C:R.126, C:D.147, C:R.213 Water bridges: C:V.113, C:R.202, C:R.213, B:Y.71 Salt bridges: C:K.90, C:R.142, C:R.142, C:R.142, C:R.213, C:R.213 ATP.13: 20 residues within 4Å: Chain B: Q.67, E.68, Y.71, N.102, S.104, G.105 Chain C: M.85, D.86, A.87, G.88, G.89, K.90, D.91, N.141, R.142, R.202, W.210, K.211 Ligands: ATP.12, MG.14 32 PLIP interactions: 23 interactions with chain C, 9 interactions with chain B Hydrogen bonds: C:M.85, C:A.87, C:G.88, C:G.89, C:K.90, C:D.91, C:N.141, C:N.141, C:R.142, C:R.142, C:R.202, B:Q.67, B:Q.67, B:Y.71, B:N.102, B:S.104 Water bridges: C:D.91, C:G.92, C:S.110, C:S.110, C:R.198, C:R.202, C:K.211, B:E.68, B:E.68, B:E.68 Salt bridges: C:K.90, C:K.90, C:R.142, C:R.202, C:K.211 pi-Stacking: B:Y.71 ATP.18: 16 residues within 4Å: Chain D: A.84, D.86, K.90, F.111, G.112, V.113, P.114, R.126, R.142, E.146, D.147, V.150, V.151, R.213 Ligands: ATP.19, MG.20 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:R.126, D:D.147, D:R.213 Water bridges: D:V.113, D:E.146, D:R.202 Salt bridges: D:K.90, D:R.142, D:R.142, D:R.142, D:R.213, D:R.213 ATP.19: 20 residues within 4Å: Chain A: Q.67, E.68, Y.71, N.102, S.104, G.105 Chain D: M.85, D.86, A.87, G.88, G.89, K.90, D.91, N.141, R.142, R.202, W.210, K.211 Ligands: ATP.18, MG.20 27 PLIP interactions: 21 interactions with chain D, 6 interactions with chain A Hydrogen bonds: D:A.87, D:A.87, D:G.88, D:G.89, D:K.90, D:D.91, D:N.141, D:N.141, D:N.141, D:R.142, D:R.142, D:R.202, A:Q.67, A:Q.67, A:N.102, A:S.104 Water bridges: D:G.92, D:S.110, D:R.198, D:R.202, A:E.68 Salt bridges: D:K.90, D:K.90, D:R.142, D:R.202, D:K.211 pi-Stacking: A:Y.71

7 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.86 Ligands: ATP.1, ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.86 MG.7: 5 residues within 4Å: Chain B: D.86, A.87, R.202 Ligands: ATP.5, ATP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.86 MG.9: 2 residues within 4Å: Chain B: T.115 Chain D: T.115 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: P.114, L.119, D.147 Ligands: ATP.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.147, H2O.13, H2O.16, H2O.18 MG.14: 4 residues within 4Å: Chain C: D.86, R.202 Ligands: ATP.12, ATP.13 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.86 MG.16: 6 residues within 4Å: Chain C: R.107, Q.129, Q.130, V.131 Chain D: R.121, W.125 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:Q.129, C:V.131, H2O.25 MG.20: 4 residues within 4Å: Chain D: D.86, A.87 Ligands: ATP.18, ATP.19 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.86

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

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 SO4.11: 5 residues within 4Å: Chain B: K.49, N.250, K.251, N.252, W.253 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.250, B:N.252, B:N.252, B:W.253 Salt bridges: B:K.49 SO4.17: 4 residues within 4Å: Chain C: K.49, K.251, N.252, W.253 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.252, C:N.252, C:W.253 Salt bridges: C:K.49 SO4.21: 4 residues within 4Å: Chain D: K.49, K.251, N.252, W.253 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.252, D:N.252, D:W.253 Salt bridges: D:K.49

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain B: Q.83, A.84, M.85, D.86, E.146, Y.226, Y.230 Ligands: ATP.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.83, B:D.86, B:E.146 Water bridges: B:A.84, B:D.219, B:Y.230 GOL.15: 7 residues within 4Å: Chain C: A.84, M.85, D.86, R.142, E.146, Y.230 Ligands: ATP.12 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.84, C:D.86, C:Y.230 Water bridges: C:A.84

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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