SMTL ID : 6aqe.1

Crystal structure of PPK2 in complex with Mg ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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 Ligands: MG.2, ATP.3, MG.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:D.66, A:D.66, A:R.106, A:E.126, A:D.127 Water bridges: A:Q.63, A:K.92, A:R.182, A:R.182, A:R.182, A:D.199, A:D.199, A:D.199 Salt bridges: A:K.70, A:K.92, A:R.122, A:R.122, A:R.122 ATP.3: 22 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, MG.4 30 PLIP interactions: 23 interactions with chain A, 7 interactions with chain B Hydrogen bonds: 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.122, A:R.182, A:K.191, B:Q.47, B:Q.47, B:N.82 Water bridges: A:G.72, A:R.182, B:Y.51, B:Y.51, 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.10: 17 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, T.131, D.196 Ligands: MG.11, ATP.12, MG.13 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:D.66, B:R.106, B:E.126, B:D.127 Water bridges: B:K.92, B:R.182, B:R.182, B:R.182, B:D.199, B:D.199, B:D.199 Salt bridges: B:K.70, B:K.92, B:R.122, B:R.122, B:R.122 ATP.12: 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.10, MG.13 30 PLIP interactions: 23 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:D.66, 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:N.82 Water bridges: B:G.72, B:R.182, B:R.182, B:K.191, A:Y.51, A:Y.51, 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

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.196 Ligands: ATP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.196, H2O.1, H2O.3, H2O.3, H2O.4 MG.4: 4 residues within 4Å: Chain A: D.66, A.67 Ligands: ATP.1, ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.66 MG.11: 2 residues within 4Å: Chain B: D.196 Ligands: ATP.10 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.196, H2O.13, H2O.13, H2O.14, H2O.16 MG.13: 3 residues within 4Å: Chain B: D.66 Ligands: ATP.10, ATP.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.66

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: K.143, E.147, R.150, T.215, T.216 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.150, A:R.150, A:T.215 Water bridges: A:K.143, A:K.143 GOL.6: 6 residues within 4Å: Chain A: P.83, A.84, V.86 Chain B: I.88, T.89, S.90 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.84, A:V.86, B:S.90 GOL.7: 5 residues within 4Å: Chain A: R.13, R.132, K.143, L.146, D.212 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.13, A:R.13, A:R.132, A:R.132, A:D.212 Water bridges: A:K.143, A:T.215 GOL.8: 5 residues within 4Å: Chain A: D.2, N.5, Y.6, D.23, A.25 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.2, A:N.5, A:D.23 GOL.14: 6 residues within 4Å: Chain B: 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

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.9: 5 residues within 4Å: Chain A: K.29, D.229, R.230, K.231, W.232 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.29, A:K.231 Hydrogen bonds: A:K.29, A:K.231, A:W.232 MPD.16: 5 residues within 4Å: Chain B: K.29, D.229, R.230, K.231, W.232 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.29, B:K.231, B:K.231, B:W.232

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.15: 3 residues within 4Å: Chain B: R.144, R.145, H.148 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B.P. et al., Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases. Acs Catalysis (2018)

Release Date

2019-01-16

Peptides

molecule A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

molecule A

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