SMTL ID : 3pnl.1 (1 other biounit)

Crystal Structure of E.coli Dha kinase DhaK-DhaL complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-oligomer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: G.53, G.54, H.57, F.79, T.80, S.81, K.105, Y.107, D.110, H.219 Chain B: R.179 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.54, A:S.81, A:K.105, A:K.105, B:R.179 Water bridges: A:S.81 GOL.5: 11 residues within 4Å: Chain C: G.53, G.54, H.57, F.79, T.80, S.81, K.105, Y.107, D.110, H.219 Chain D: R.179 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.54, C:S.81, C:K.105, C:K.105, D:R.179 Water bridges: C:S.81

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

ADP.2: 23 residues within 4Å: Chain A: T.108 Chain B: D.31, D.36, D.38, H.39, N.42, G.79, A.80, S.81, L.84, G.122, A.124, T.130, M.131, K.177, G.178, R.179, D.192, P.193, G.194, A.195 Ligands: MG.3, MG.4 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.80, B:S.81, B:G.122, B:M.131, B:D.192, B:G.194, B:A.195, A:T.108 Water bridges: B:D.31, B:D.36, B:A.124, B:G.178, B:G.178, B:R.179, B:R.179, B:R.179, B:R.179 Salt bridges: B:H.39, B:R.179 ADP.6: 23 residues within 4Å: Chain C: T.108 Chain D: D.31, D.36, D.38, H.39, N.42, G.79, A.80, S.81, L.84, G.122, A.124, T.130, M.131, K.177, G.178, R.179, D.192, P.193, G.194, A.195 Ligands: MG.7, MG.8 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:A.80, D:S.81, D:G.122, D:T.130, D:M.131, D:D.192, D:G.194, D:A.195 Water bridges: D:D.31, D:D.31, D:D.36, D:A.124, D:G.178, D:G.178, D:R.179, D:R.179, D:R.179, D:R.179 Salt bridges: D:H.39, D:R.179

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain B: D.31, D.36, D.38, H.39 Ligands: ADP.2, MG.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.31, B:D.36, B:D.38, H2O.7 MG.4: 7 residues within 4Å: Chain A: F.79, T.80 Chain B: D.36, D.38, R.179 Ligands: ADP.2, MG.3 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.36, B:D.38, A:F.79, H2O.6 MG.7: 6 residues within 4Å: Chain D: D.31, D.36, D.38, H.39 Ligands: ADP.6, MG.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.31, D:D.36, D:D.38, H2O.15 MG.8: 7 residues within 4Å: Chain C: F.79, T.80 Chain D: D.36, D.38, R.179 Ligands: ADP.6, MG.7 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:D.36, D:D.38, C:F.79, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, R. et al., Structural and mechanistic insight into covalent substrate binding by Escherichia coli dihydroxyacetone kinase. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-01-12

Peptides

PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK: AC
PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK

PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL

Related Entries With Identical Sequence