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

Crystal Structure of a Hyperactive Escherichia coli Glycerol Kinase Mutant Gly230 --> Asp Obtained Using Microfluidic Crystallization Devices

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: T.13, Q.82, R.83, E.84, W.103, Y.135, D.245, Q.246, F.270 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.13, A:R.83, A:R.83, A:R.83, A:Y.135, A:Q.246 GOL.6: 9 residues within 4Å: Chain B: T.13, Q.82, R.83, E.84, W.103, Y.135, D.245, Q.246, F.270 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.13, B:T.13, B:R.83, B:R.83, B:R.83, B:Y.135, B:Y.135, B:Q.246 GOL.10: 9 residues within 4Å: Chain C: T.13, Q.82, R.83, E.84, W.103, Y.135, D.245, Q.246, F.270 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.83, C:R.83, C:E.84, C:Y.135, C:D.245, C:Q.246 Water bridges: C:T.13, C:T.13 GOL.13: 9 residues within 4Å: Chain D: T.13, Q.82, R.83, E.84, W.103, Y.135, D.245, Q.246, F.270 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.83, D:R.83, D:E.84, D:D.245, D:Q.246 Water bridges: D:T.13, D:D.245

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

CL.2: 4 residues within 4Å: Chain A: R.177, V.178, G.225, Q.226 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: R.177, V.178, G.225, Q.226 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain C: T.174, R.177, V.178, G.225, Q.226 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain D: R.177, V.178, G.225, Q.226 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.72 Chain D: K.232 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.72, H2O.1, H2O.1, H2O.1, H2O.1, H2O.26

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

EDO.4: 5 residues within 4Å: Chain A: H.195, E.277, K.278, A.279, Y.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.195, A:E.277, A:A.279 EDO.5: 8 residues within 4Å: Chain A: V.306, L.351, G.352, A.353, Y.355, Q.387, D.390, W.486 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.352, A:D.390, A:D.390 Water bridges: A:Q.387 EDO.8: 5 residues within 4Å: Chain B: H.195, E.277, K.278, A.279, Y.300 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.195, B:A.279 EDO.9: 8 residues within 4Å: Chain B: A.109, C.112, E.113, K.116, I.132, D.133, P.134, P.358 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.116, B:K.116 EDO.12: 5 residues within 4Å: Chain C: K.116, E.121, R.125, V.131, W.356 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.116, C:K.116, C:R.125 Water bridges: C:I.132 EDO.15: 4 residues within 4Å: Chain D: E.121, R.125, V.131, W.356 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.116, D:K.116, D:R.125 Water bridges: D:R.125 EDO.16: 5 residues within 4Å: Chain D: H.195, E.277, K.278, A.279, Y.300 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.195, D:A.279 EDO.17: 9 residues within 4Å: Chain D: A.305, V.306, L.351, G.352, A.353, P.354, Y.355, Q.387, D.390 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.352, D:G.352, D:D.390, D:D.390 EDO.18: 6 residues within 4Å: Chain D: T.339, V.342, Y.343, E.382, Y.386, R.482 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.382, D:Y.386, D:R.482 Water bridges: D:T.339, D:T.339, D:T.339, D:E.382

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anderson, M.J. et al., Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices. Biochemistry (2007)

Release Date

2008-11-04

Peptides

Glycerol kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
G

Glycerol kinase

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