SMTL ID : 7plj.1 (1 other biounit)

Structure of Polyphosphate kinase 2 from Deinococcus radiodurans, in complex with ATP and polyphosphates.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

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

ATP.1: 15 residues within 4Å: Chain A: A.64, D.66, K.70, F.91, K.92, Q.93, P.94, R.106, R.122, E.126, D.127, V.130, N.193 Ligands: ATP.2, MG.7 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.64, A:R.106, A:E.126, A:D.127, A:N.193 Water bridges: A:K.92, A:K.92, A:Q.93, A:R.182, A:D.199, A:D.199, A:D.199, B:Y.51 Salt bridges: A:K.70, A:K.92, A:R.122, A:R.122, A:R.122 ATP.2: 23 residues within 4Å: Chain A: R.65, D.66, A.67, A.68, G.69, K.70, D.71, S.90, K.92, N.121, R.122, R.182, W.190, K.191 Chain B: Q.47, E.48, Y.51, N.82, A.84, G.85 Ligands: ATP.1, 3PO.4, MG.7 28 PLIP interactions: 22 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:A.67, A:A.67, A:A.68, A:G.69, A:K.70, A:D.71, A:S.90, A:K.92, A:N.121, A:R.122, A:R.122, A:R.182, B:Q.47, B:Q.47, B:E.48, B:N.82 Water bridges: A:R.182, A:R.182, A:K.191, A:K.191, B:N.82 Salt bridges: A:K.70, A:K.70, A:R.122, A:R.182, A:K.191 pi-Stacking: A:W.190, B:Y.51 ATP.8: 15 residues within 4Å: Chain B: A.64, D.66, K.70, F.91, K.92, Q.93, P.94, R.106, R.122, E.126, D.127, V.130, N.193 Ligands: ATP.9, MG.14 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:A.64, B:D.66, B:R.106, B:E.126, B:D.127, B:N.193 Water bridges: B:R.182, B:D.199, B:D.199 Salt bridges: B:K.70, B:K.92, B:R.122, B:R.122, B:R.122 ATP.9: 22 residues within 4Å: Chain A: Q.47, E.48, Y.51, N.82, A.84, G.85 Chain B: R.65, D.66, A.67, A.68, G.69, K.70, D.71, S.90, K.92, N.121, R.122, R.182, W.190, K.191 Ligands: ATP.8, MG.14 26 PLIP interactions: 6 interactions with chain A, 20 interactions with chain B Hydrogen bonds: A:Q.47, A:Q.47, A:E.48, A:N.82, B:A.67, B:A.68, B:G.69, B:K.70, B:D.71, B:S.90, B:S.90, B:K.92, B:N.121, B:R.122, B:R.182, B:K.191 Water bridges: A:N.82, B:G.72, B:R.182 pi-Stacking: A:Y.51, B:W.190 Salt bridges: B:K.70, B:K.70, B:R.122, B:R.182, B:K.191

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

ADP.3: 6 residues within 4Å: Chain A: N.5, K.9, K.12, R.13, D.18, W.19 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.5, A:R.13 Water bridges: A:A.20, A:A.20 Salt bridges: A:K.9, A:K.9, A:K.12 pi-Stacking: A:W.19, A:W.19

1 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.4: 10 residues within 4Å: Chain A: G.69, D.71, G.72, K.75, K.188, K.191, K.231, R.234 Ligands: ATP.2, 7TT.5 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:D.71, A:D.71, A:D.71, A:G.72 Water bridges: A:D.71, A:R.178, A:R.182, A:R.182, A:K.188, A:K.231, A:K.231, A:K.231, A:K.231, A:R.234, A:R.234 Salt bridges: A:K.75, A:K.75, A:K.188, A:K.191, A:K.191, A:K.231, A:R.234

1 x 7TT: Tetraphosphate(Non-covalent)

7TT.5: 5 residues within 4Å: Chain A: K.29, Q.33, K.231, W.232 Ligands: 3PO.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.231, A:W.232 Water bridges: A:Q.33, A:Q.33, A:K.231, A:K.231, A:K.231 Salt bridges: A:K.29, A:K.29, A:K.75, A:K.231, A:K.231

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: S.90, F.91, K.92, E.98, R.106, K.110 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.90, A:K.92, A:E.98, A:R.106, A:K.110, A:K.110 Water bridges: A:S.95 GOL.10: 6 residues within 4Å: Chain B: K.29, R.178, D.229, R.230, K.231, W.232 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.178, B:D.229, B:K.231, B:W.232 GOL.13: 2 residues within 4Å: Chain B: E.147, H.151 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.147 Water bridges: B:H.151

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain A: D.66 Ligands: ATP.1, ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.66 MG.14: 5 residues within 4Å: Chain B: D.66, A.67, R.182 Ligands: ATP.8, ATP.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.66

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 2 residues within 4Å: Chain B: N.5, W.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.5 Water bridges: B:A.20

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.12: 6 residues within 4Å: Chain B: D.71, K.75, R.182, K.188, K.191, K.231 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.71, B:R.182 Water bridges: B:G.72, B:R.182, B:K.231, B:K.231 Salt bridges: B:K.75, B:K.188, B:K.188, B:K.191, B:K.191, B:K.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silva, S.T.N. et al., Structure of Polyphosphate kinase 2 from Deinococcus radiodurans, in complex with ATP and polyphosphates. To Be Published

Release Date

2023-03-22

Peptides

PPK2 domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PPK2 domain-containing protein

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