SMTL ID : 7plj.2 (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: 14 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 Ligands: ATP.2, MG.8 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:D.66, A:R.106, A:E.126, A:E.126, A:D.127 Water bridges: A:A.64, A:D.66, A:D.66, A:D.66, A:D.127, A:D.127, A:R.182, A:R.182, A:D.196, A:D.199 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, PPV.3, MG.8 28 PLIP interactions: 23 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.66, A:D.66, A:A.67, A:A.68, A:G.69, A:K.70, A:D.71, A:S.90, A:S.90, A:K.92, A:N.121, A:N.121, A:R.122, A:R.182, A:K.191, B:Q.47, B:E.48, B:N.82 Water bridges: A:G.72, A:R.182, 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.9: 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.10, MG.17 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:A.64, B:R.106, B:E.126, B:E.126, B:D.127 Water bridges: B:Q.63, B:D.66, B:D.66, B:D.66, B:D.127, B:D.127, B:R.182, B:R.182, B:D.196, B:D.199 Salt bridges: B:K.70, B:K.92, B:R.122, B:R.122, B:R.122 ATP.10: 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.9, MG.17 29 PLIP interactions: 23 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:A.67, 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.122, B:R.182, A:Q.47, A:Q.47, A:Y.51, A:N.82 Water bridges: B:G.72, B:R.182, B:R.182, B:K.191, A:N.82 Salt bridges: B:K.70, B:K.70, B:R.122, B:R.182, B:K.191 pi-Stacking: B:W.190, A:Y.51

2 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.3: 7 residues within 4Å: Chain A: D.71, K.75, K.188, K.191 Chain B: E.48, N.82 Ligands: ATP.2 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Water bridges: A:K.75, A:K.75, A:K.188, A:K.188 Salt bridges: A:K.75, A:K.75, A:K.188, A:K.188, A:K.191, A:K.191 Hydrogen bonds: B:E.48, B:E.48, B:N.82 PPV.4: 5 residues within 4Å: Chain A: K.29, D.229, R.230, K.231, W.232 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.231, A:W.232 Water bridges: A:E.174, A:R.178, A:D.229, A:D.229 Salt bridges: A:K.29, A:K.29

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

PEG.5: 4 residues within 4Å: Chain A: Y.51, A.52, Y.116, P.254 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.114 PEG.7: 6 residues within 4Å: Chain A: L.16, S.17, W.19, H.169, W.203, N.207 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.19, A:W.19, A:N.207 PEG.13: 3 residues within 4Å: Chain B: R.144, E.147, H.151 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.144 Water bridges: B:R.144 PEG.15: 3 residues within 4Å: Chain B: K.75, R.182, K.191 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.75, B:K.75, B:R.182, B:R.182, B:K.191 Water bridges: B:R.234

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: D.66, L.179, R.182, K.191, F.192, N.193, D.196, L.197 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.182, A:K.191, A:N.193 Water bridges: A:D.196, A:D.196 GOL.11: 7 residues within 4Å: Chain B: T.89, S.90, F.91, K.92, E.98, R.106, K.110 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.90, B:K.92, B:E.98, B:R.106, B:K.110, B:K.110 Water bridges: B:S.95 GOL.14: 5 residues within 4Å: Chain B: Y.51, A.52, G.54, K.114, Y.116 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.52, B:K.114

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain A: D.66, R.182 Ligands: ATP.1, ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.66 MG.17: 5 residues within 4Å: Chain B: D.66, A.67, R.182 Ligands: ATP.9, ATP.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.66

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

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

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

PO4.16: 4 residues within 4Å: Chain B: K.29, R.230, K.231, W.232 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.229, B:K.231, B:W.232 Water bridges: B:W.232 Salt bridges: B:K.29

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
C

B
D

PPK2 domain-containing protein

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