SMTL ID : 5llb.1

Structure of Polyphosphate Kinase 2 from Francisella tularensis with AMPPCH2PPP and polyphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

hetero-2-2-mer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: R.61, W.163, S.165, V.166, K.206 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: R.61, W.163, S.165, K.206 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain C: R.61, W.163, S.165, V.166, K.206 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain D: R.61, W.163, S.165, V.166, K.206 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.62, R.118, S.189, D.192 Ligands: 6YZ.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.62, A:D.192 MG.6: 6 residues within 4Å: Chain B: D.62, R.118, R.178, S.189, D.192 Ligands: 6YZ.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.192 MG.10: 6 residues within 4Å: Chain C: D.62, R.118, S.189, I.191, D.192 Ligands: 6YZ.11 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.62, C:D.192, H2O.13 MG.14: 6 residues within 4Å: Chain D: D.62, R.118, S.189, I.191, D.192 Ligands: 6YZ.15 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.62, D:D.192, H2O.21

4 x 6YZ: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]methyl]phosphinic acid(Non-covalent)

6YZ.3: 22 residues within 4Å: Chain A: D.62, A.63, A.64, G.65, K.66, G.67, L.87, E.88, K.89, P.90, R.118, N.122, V.126, E.127, F.132, R.178, K.187, S.189, I.191, D.192 Chain C: R.80 Ligands: MG.2 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:D.62, A:A.63, A:A.64, A:G.65, A:K.66, A:G.67, A:E.88, A:K.89, A:K.89, A:R.118, A:R.118, A:N.122, A:S.189 Water bridges: A:G.68, A:L.87, A:L.87, A:N.122, A:R.178, A:R.178, A:K.187 Salt bridges: A:K.66, A:K.66, A:R.118, A:R.178, A:R.178 6YZ.7: 23 residues within 4Å: Chain B: R.61, D.62, A.63, A.64, G.65, K.66, G.67, L.87, E.88, K.89, P.90, R.118, N.122, V.126, E.127, F.132, R.178, K.187, S.189, I.191, D.192 Chain D: R.80 Ligands: MG.6 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:A.63, B:A.64, B:G.65, B:K.66, B:G.67, B:L.87, B:R.118, B:R.118, B:N.122, B:S.189 Water bridges: B:G.68, B:L.87, B:L.87, B:Y.103, B:N.122 Salt bridges: B:K.66, B:K.66, B:R.118, B:R.178, B:R.178 6YZ.11: 22 residues within 4Å: Chain A: R.80 Chain C: R.61, D.62, A.63, A.64, G.65, K.66, G.67, L.87, E.88, K.89, P.90, R.118, N.122, V.126, E.127, F.132, R.178, S.189, I.191, D.192 Ligands: MG.10 25 PLIP interactions: 22 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:D.62, C:D.62, C:D.62, C:A.63, C:A.64, C:G.65, C:K.66, C:K.66, C:G.67, C:E.88, C:R.118, C:R.118, C:N.122, C:S.189 Water bridges: C:G.68, C:R.178, C:R.178, C:R.178, A:R.80, A:R.80, A:R.80 Salt bridges: C:K.66, C:K.66, C:R.178, C:R.178 6YZ.15: 22 residues within 4Å: Chain B: R.80 Chain D: D.62, A.63, A.64, G.65, K.66, G.67, L.87, E.88, K.89, P.90, R.118, N.122, V.126, E.127, F.132, R.178, K.187, S.189, I.191, D.192 Ligands: MG.14 27 PLIP interactions: 26 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:D.62, D:D.62, D:A.63, D:A.64, D:G.65, D:K.66, D:K.66, D:G.67, D:R.118, D:R.118, D:N.122, D:S.189, B:R.80 Water bridges: D:G.68, D:L.87, D:Y.103, D:N.122, D:E.127, D:R.178, D:R.178, D:K.187, D:K.187, D:I.191 Salt bridges: D:K.66, D:K.66, D:R.178, D:R.178

4 x 6YW: [oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

6YW.4: 12 residues within 4Å: Chain A: Y.29, E.30, K.33, G.65, G.68, R.72, R.178, K.184, K.187, K.228, K.229, R.232 26 PLIP interactions: 25 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.29, A:Y.29, A:R.178, A:R.232 Water bridges: A:K.33, A:G.68, A:K.228, A:K.228, A:R.232, C:H.76 Salt bridges: A:K.33, A:R.72, A:R.72, A:R.72, A:R.72, A:K.184, A:K.184, A:K.187, A:K.187, A:K.228, A:K.228, A:K.228, A:K.229, A:K.229, A:R.232, A:R.232 6YW.8: 13 residues within 4Å: Chain B: R.26, Y.29, E.30, K.33, G.65, G.68, K.71, R.72, K.184, K.187, K.228, K.229, R.232 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:Y.29, B:Y.29, B:E.30, B:R.232 Water bridges: B:G.65, B:G.68, B:R.178 Salt bridges: B:R.26, B:R.26, B:K.33, B:R.72, B:R.72, B:R.72, B:R.72, B:K.184, B:K.184, B:K.184, B:K.187, B:K.228, B:K.228, B:K.228, B:K.229, B:K.229, B:R.232, B:R.232, B:R.232 6YW.12: 13 residues within 4Å: Chain C: R.26, Y.29, E.30, K.33, G.65, G.68, R.72, R.178, K.184, K.187, K.228, K.229, R.232 23 PLIP interactions: 23 interactions with chain C Hydrogen bonds: C:Y.29, C:R.232 Water bridges: C:G.65, C:G.68 Salt bridges: C:R.26, C:R.26, C:K.33, C:R.72, C:R.72, C:R.72, C:R.72, C:R.72, C:K.184, C:K.187, C:K.228, C:K.228, C:K.228, C:K.229, C:K.229, C:R.232, C:R.232, C:R.232, C:R.232 6YW.16: 14 residues within 4Å: Chain B: H.76 Chain D: R.26, Y.29, E.30, K.33, G.65, G.68, R.72, R.178, K.184, K.187, K.228, K.229, R.232 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:Y.29, D:E.30, D:G.68 Water bridges: D:R.232 Salt bridges: D:R.26, D:R.26, D:K.33, D:R.72, D:R.72, D:R.72, D:R.72, D:K.184, D:K.184, D:K.187, D:K.187, D:K.228, D:K.228, D:K.228, D:K.228, D:K.229, D:K.229, D:R.232, D:R.232, D:R.232, D:R.232

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

2017-10-11

Peptides

Polyphosphate kinase 2: AB
Polyphosphate kinase 2: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Polyphosphate kinase 2

Polyphosphate kinase 2

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