SMTL ID : 5llf.2 (1 other biounit)

Structure of Polyphosphate Kinase 2 mutant D117N from Francisella tularensis with polyphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-dimer

Ligands

1 x 6YY: bis[oxidanyl-[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl]oxy-phosphoryl] hydrogen phosphate(Non-covalent)

6YY.1: 16 residues within 4Å: Chain A: R.26, R.61, A.63, A.64, G.65, K.66, G.67, G.68, R.72, R.174, R.178, K.184, K.187, K.228, K.229, R.232 35 PLIP interactions: 35 interactions with chain A Hydrogen bonds: A:R.26, A:A.63, A:A.64, A:G.65, A:K.66, A:G.67, A:G.68, A:R.178 Water bridges: A:N.117, A:N.117, A:K.228, A:K.228, A:K.228, A:K.228 Salt bridges: A:R.26, A:K.66, A:R.72, A:R.72, A:R.178, A:R.178, A:K.184, A:K.184, A:K.187, A:K.187, A:K.187, A:K.228, A:K.228, A:K.228, A:K.228, A:K.228, A:K.229, A:K.229, A:K.229, A:R.232, A:R.232

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

CL.2: 2 residues within 4Å: Chain A: R.9, T.263 Ligand excluded by PLIP

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

PO4.3: 7 residues within 4Å: Chain A: N.16, R.61, W.163, S.165, V.166, W.199, K.206 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.16, A:N.16, A:N.16, A:W.163, A:V.166 Water bridges: A:S.165, A:S.165 Salt bridges: A:R.61, A:K.206 PO4.4: 6 residues within 4Å: Chain A: R.26, Y.29, E.30, K.33, R.72, R.232 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.30, A:R.232 Water bridges: A:K.33, A:K.33 Salt bridges: A:R.26, A:K.33, A:R.72 PO4.6: 7 residues within 4Å: Chain B: N.16, R.61, W.163, S.165, V.166, W.199, K.206 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.16, B:N.16, B:W.163 Water bridges: B:N.16, B:V.166, B:T.203, B:T.203, B:K.206 Salt bridges: B:R.61, B:K.206 PO4.7: 4 residues within 4Å: Chain B: Y.29, K.33, R.72, R.232 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.29, B:E.30, B:R.232 Salt bridges: B:K.33, B:R.72

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

6YW.5: 13 residues within 4Å: Chain B: D.62, A.63, A.64, G.65, K.66, G.67, G.68, R.72, R.178, K.184, K.187, K.228, R.232 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:A.63, B:A.64, B:G.65, B:K.66, B:G.67, B:G.68 Water bridges: B:K.228, B:R.232 Salt bridges: B:K.66, B:R.72, B:R.72, B:K.184, B:K.184, B:K.184, B:K.187, B:K.187, B:K.187, B:K.187, B:K.228, B:K.228, B:K.228, B:K.228, B:K.228, B:R.232, B: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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Polyphosphate kinase 2

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