SMTL ID : 1glf.1

CRYSTAL STRUCTURES OF ESCHERICHIA COLI GLYCEROL KINASE AND THE MUTANT A65T IN AN INACTIVE TETRAMER: CONFORMATIONAL CHANGES AND IMPLICATIONS FOR ALLOSTERIC REGULATION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 9 residues within 4Å: Chain A: N.228, G.233, G.234, R.236 Chain D: N.228, G.233, G.234, T.235, R.236 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:G.234, D:N.228, D:G.234, D:T.235 Water bridges: A:N.228, A:T.235, D:R.236 Salt bridges: A:R.236, D:R.236 PO4.4: 9 residues within 4Å: Chain B: N.228, G.233, G.234, T.235, R.236 Chain C: N.228, G.233, G.234, R.236 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.234, B:T.235, C:N.228, C:G.234 Water bridges: B:N.228, B:G.230, B:R.236 Salt bridges: B:R.236, C:R.236

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

ADP.2: 16 residues within 4Å: Chain A: G.12, T.13, R.17, G.266, T.267, G.310, A.311, I.313, Q.314, A.326, Y.327, S.329, G.411, A.412, A.414, N.415 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.13, A:T.267, A:T.267, A:Q.314, A:S.329, A:G.411, A:N.415 Water bridges: A:D.10, A:R.17, A:R.17, A:R.17, A:R.17, A:R.17 Salt bridges: A:R.17, A:R.17 ADP.5: 14 residues within 4Å: Chain B: G.12, T.13, R.17, G.266, T.267, G.310, A.311, I.313, A.326, Y.327, G.410, G.411, A.412, N.415 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:T.13, B:T.267, B:T.267, B:G.411, B:N.415, B:N.415 Water bridges: B:R.17, B:D.245, B:T.267, B:T.267 Salt bridges: B:R.17, B:R.17 ADP.7: 15 residues within 4Å: Chain C: G.12, T.13, R.17, G.266, T.267, G.310, A.311, I.313, A.326, Y.327, S.329, G.410, G.411, A.412, N.415 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:T.13, C:T.267, C:S.329, C:G.411, C:A.412 Water bridges: C:T.14, C:T.14, C:R.17, C:D.245, C:T.267, C:T.267, C:Y.327, C:N.415 Salt bridges: C:R.17, C:R.17 ADP.9: 15 residues within 4Å: Chain D: G.12, T.13, R.17, Y.265, G.266, T.267, G.310, A.311, I.313, A.326, Y.327, S.329, G.411, A.412, N.415 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:T.13, D:T.267, D:T.267, D:T.267, D:S.329, D:G.411 Water bridges: D:T.14, D:R.17, D:R.17, D:D.245, D:T.267, D:A.326, D:S.329 Salt bridges: D:R.17, D:R.17

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: T.13, N.81, 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:E.84, A:Q.246 GOL.6: 10 residues within 4Å: Chain B: T.13, N.81, Q.82, R.83, E.84, W.103, Y.135, D.245, Q.246, F.270 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.83, B:R.83, B:E.84, B:Y.135, B:Q.246 Water bridges: B:T.13, B:T.13 GOL.8: 9 residues within 4Å: Chain C: N.81, Q.82, R.83, E.84, W.103, Y.135, D.245, Q.246, F.270 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.83, C:R.83, C:E.84, C:Q.246 Water bridges: C:T.13, C:T.267 GOL.10: 10 residues within 4Å: Chain D: T.13, Q.82, R.83, E.84, W.103, Y.135, R.188, D.245, Q.246, F.270 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.13, D:R.83, D:R.83, D:R.83, D:E.84, D:R.188, D:Q.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feese, M.D. et al., Glycerol kinase from Escherichia coli and an Ala65-->Thr mutant: the crystal structures reveal conformational changes with implications for allosteric regulation. Structure (1998)

Release Date

1998-10-16

Peptides

PROTEIN (GLYCEROL KINASE): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
Y

C
Z

D
X

PROTEIN (GLYCEROL KINASE)

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