SMTL ID : 1igw.1

Crystal Structure of the Isocitrate Lyase from the A219C mutant of Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

21 x HG: MERCURY (II) ION(Non-covalent)

HG.1: 4 residues within 4Å: Chain A: P.41, E.42, C.43, E.177 Ligand excluded by PLIP HG.2: 4 residues within 4Å: Chain A: F.169, K.173, C.219, T.223 Ligand excluded by PLIP HG.3: 4 residues within 4Å: Chain A: C.245, D.246 Chain B: S.259, E.260 Ligand excluded by PLIP HG.4: 2 residues within 4Å: Chain A: C.288, T.290 Ligand excluded by PLIP HG.5: 3 residues within 4Å: Chain A: Y.316, C.318 Chain D: M.375 Ligand excluded by PLIP HG.8: 4 residues within 4Å: Chain B: P.41, E.42, C.43, E.177 Ligand excluded by PLIP HG.9: 4 residues within 4Å: Chain B: F.169, K.173, C.219, T.223 Ligand excluded by PLIP HG.10: 3 residues within 4Å: Chain A: E.260 Chain B: C.245, D.246 Ligand excluded by PLIP HG.11: 2 residues within 4Å: Chain B: C.288, T.290 Ligand excluded by PLIP HG.12: 5 residues within 4Å: Chain B: N.317, C.318, F.349, I.350 Chain C: M.375 Ligand excluded by PLIP HG.15: 4 residues within 4Å: Chain C: P.41, E.42, C.43, E.177 Ligand excluded by PLIP HG.16: 4 residues within 4Å: Chain C: F.169, K.173, C.219, T.223 Ligand excluded by PLIP HG.17: 4 residues within 4Å: Chain C: C.245, D.246 Chain D: S.259, E.260 Ligand excluded by PLIP HG.18: 2 residues within 4Å: Chain C: C.288, T.290 Ligand excluded by PLIP HG.19: 5 residues within 4Å: Chain B: M.375 Chain C: N.317, C.318, F.349, I.350 Ligand excluded by PLIP HG.20: 4 residues within 4Å: Chain B: Q.416 Chain C: C.195, G.196, H.197 Ligand excluded by PLIP HG.23: 4 residues within 4Å: Chain D: P.41, E.42, C.43, E.177 Ligand excluded by PLIP HG.24: 4 residues within 4Å: Chain D: F.169, K.173, C.219, T.223 Ligand excluded by PLIP HG.25: 4 residues within 4Å: Chain C: S.259, E.260 Chain D: C.245, D.246 Ligand excluded by PLIP HG.26: 3 residues within 4Å: Chain D: C.288, E.289, T.290 Ligand excluded by PLIP HG.27: 6 residues within 4Å: Chain A: M.375 Chain D: N.317, C.318, Q.337, F.349, I.350 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: D.157 Ligands: PYR.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.157, H2O.8, H2O.8, H2O.8 MG.13: 2 residues within 4Å: Chain B: D.157 Ligands: PYR.14 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.157, H2O.15, H2O.15, H2O.15 MG.21: 2 residues within 4Å: Chain C: D.157 Ligands: PYR.22 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.157, H2O.25, H2O.25, H2O.25 MG.28: 5 residues within 4Å: Chain D: G.92, W.93, D.108, D.157 Ligands: PYR.29 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.157, H2O.30, H2O.30, H2O.30

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.7: 10 residues within 4Å: Chain A: Y.89, S.91, G.92, W.93, D.157, H.184, R.232, T.351, L.352 Ligands: MG.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.351 Hydrogen bonds: A:G.92, A:W.93, A:D.157, A:D.157, A:R.232, A:T.351 Water bridges: A:E.289 PYR.14: 10 residues within 4Å: Chain B: Y.89, S.91, G.92, W.93, D.157, H.184, R.232, W.287, T.351 Ligands: MG.13 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.287, B:T.351 Hydrogen bonds: B:G.92, B:W.93, B:D.157, B:R.232, B:T.351 Water bridges: B:R.232, B:T.351 PYR.22: 10 residues within 4Å: Chain C: Y.89, S.91, G.92, W.93, D.157, H.184, R.232, W.287, T.351 Ligands: MG.21 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.287, C:T.351 Hydrogen bonds: C:Y.89, C:G.92, C:W.93, C:D.157, C:R.232 Water bridges: C:R.232 PYR.29: 11 residues within 4Å: Chain D: Y.89, S.91, G.92, W.93, D.157, H.184, R.232, W.287, T.351, L.352 Ligands: MG.28 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:T.351 Hydrogen bonds: D:Y.89, D:G.92, D:W.93, D:D.157, D:R.232 Water bridges: D:R.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Britton, K.L. et al., The structure and domain organization of Escherichia coli isocitrate lyase. Acta Crystallogr.,Sect.D (2001)

Release Date

2001-09-05

Peptides

Isocitrate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isocitrate lyase