SMTL ID : 3czp.1

Crystal structure of putative polyphosphate kinase 2 from Pseudomonas aeruginosa PA01

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 2 residues within 4Å: Chain A: S.461, T.462 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.461 ACT.2: 4 residues within 4Å: Chain A: R.140, R.205, D.206, Y.207 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.206, A:Y.207 Hydrogen bonds: A:R.140, A:D.206 Salt bridges: A:R.205 ACT.3: 4 residues within 4Å: Chain A: L.149, F.150, P.209, Y.211 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.207, A:Y.211 Water bridges: A:L.149 ACT.4: 4 residues within 4Å: Chain A: R.96 Chain B: E.83, R.87, W.91 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Water bridges: A:S.81 Salt bridges: A:R.95, A:R.96, B:R.87 Hydrophobic interactions: B:W.91 Hydrogen bonds: B:E.83 ACT.10: 5 residues within 4Å: Chain B: H.299, S.400, G.403, I.404, A.493 4 PLIP interactions: 4 interactions with chain B Water bridges: B:S.400, B:S.400 Salt bridges: B:H.299, B:K.496

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 3 residues within 4Å: Chain A: R.140, D.144, Y.207 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.140, A:C.143, A:D.144 EDO.12: 4 residues within 4Å: Chain A: P.333 Chain B: K.37, R.70, L.71 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.37 EDO.13: 6 residues within 4Å: Chain B: N.308, D.309, Q.418, N.442, R.443, Y.449 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.308, B:D.309, B:D.309, B:Q.418 Water bridges: B:D.309

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: V.22, I.23, R.26, E.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.26, A:E.27 GOL.7: 6 residues within 4Å: Chain A: A.21, E.24, L.25, R.227, L.230 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.24, A:R.227 GOL.8: 6 residues within 4Å: Chain A: E.24, L.25, A.28, L.230, Q.234 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.234 Water bridges: A:A.28 GOL.9: 7 residues within 4Å: Chain A: D.309, A.310, A.311, G.312, K.313, G.314, R.425 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.310, A:A.311, A:G.312, A:K.313, A:R.425

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.11: 7 residues within 4Å: Chain A: R.70 Chain B: N.308, A.310, A.311, G.312, K.313, G.314 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B Water bridges: A:R.70, B:K.313, B:G.315 Salt bridges: A:R.70, B:K.313 Hydrogen bonds: B:A.310, B:A.311, B:G.312, B:K.313, B:G.314

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B. et al., Polyphosphate-dependent synthesis of ATP and ADP by the family-2 polyphosphate kinases in bacteria. Proc.Natl.Acad.Sci.USA (2008)

Release Date

2008-07-01

Peptides

Putative polyphosphate kinase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative polyphosphate kinase 2