SMTL ID : 2j5t.1 (5 other biounits)

Glutamate 5-kinase from Escherichia coli complexed with glutamate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

6 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 7 residues within 4Å: Chain A: D.281, G.283, A.284, S.294, L.296, K.298, G.299 8 PLIP interactions: 4 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: A:A.284 Hydrogen bonds: A:L.296, A:G.299, E.1, E.1, E.1, E.1 Salt bridges: A:K.298 GLU.2: 8 residues within 4Å: Chain A: S.50, G.51, A.52, I.53, N.134, D.137, D.148, N.149 9 PLIP interactions: 9 interactions with chain A, Hydrogen bonds: A:S.50, A:G.51, A:A.52, A:I.53, A:N.134, A:N.134, A:D.137, A:N.149 Salt bridges: A:K.10 GLU.8: 9 residues within 4Å: Chain B: S.50, G.51, A.52, I.53, N.134, E.135, D.137, D.148, N.149 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:S.50, B:G.51, B:A.52, B:I.53, B:N.134, B:N.134, B:D.137, B:N.149, B:N.149, E.8 Salt bridges: B:K.10 GLU.14: 8 residues within 4Å: Chain C: S.50, G.51, A.52, I.53, N.134, D.137, D.148, N.149 11 PLIP interactions: 10 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:S.50, C:S.50, C:G.51, C:A.52, C:I.53, C:N.134, C:N.134, C:D.137, C:N.149, E.14 Salt bridges: C:K.10 GLU.19: 8 residues within 4Å: Chain D: D.281, G.283, A.284, A.287, R.291, S.294, L.296, G.299 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:R.291, D:L.296, D:G.299, E.19, E.19 GLU.20: 8 residues within 4Å: Chain D: S.50, G.51, A.52, I.53, N.134, D.137, D.148, N.149 11 PLIP interactions: 10 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: D:S.50, D:S.50, D:G.51, D:A.52, D:I.53, D:N.134, D:N.134, D:D.137, D:N.149, E.20 Salt bridges: D:K.10

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 7 residues within 4Å: Chain A: G.12, T.13, S.14, L.168, T.169, D.170, K.217 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.14, A:S.14, A:S.14 Water bridges: A:K.10, A:T.13 Salt bridges: A:K.10, A:K.217 SO4.9: 8 residues within 4Å: Chain B: K.10, G.12, T.13, S.14, L.168, T.169, D.170, K.217 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.12, B:S.14, B:S.14, B:S.14, B:T.169, B:D.170 Salt bridges: B:K.10, B:K.217 SO4.15: 7 residues within 4Å: Chain C: G.12, T.13, S.14, L.168, T.169, D.170, K.217 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.14, C:S.14, C:L.168, C:T.169, C:D.170 Water bridges: C:K.217 Salt bridges: C:K.10, C:K.217 SO4.22: 9 residues within 4Å: Chain D: K.10, G.12, T.13, S.14, V.15, L.168, T.169, D.170, K.217 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.12, D:S.14, D:S.14, D:V.15, D:D.170 Salt bridges: D:K.10, D:K.217

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

CL.4: 2 residues within 4Å: Chain A: P.261, R.267 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: R.33, Q.37 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: R.111, R.265 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: R.82, Q.85 Chain B: E.88 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: R.33, Q.37 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: R.267 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain C: R.33, Q.37 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain C: D.196 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain C: R.267 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain D: R.33 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain D: R.267 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 1 residues within 4Å: Chain A: N.306 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain B: E.311 No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Chain D: D.204 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.204, D:D.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marco-Marin, C. et al., A Novel Two-Domain Architecture within the Amino Acid Kinase Enzyme Family Revealed by the Crystal Structure of Escherichia Coli Glutamate 5-Kinase. J.Mol.Biol. (2007)

Release Date

2007-03-06

Peptides

GLUTAMATE 5-KINASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GLUTAMATE 5-KINASE

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