SMTL ID : 7ebe.1 (1 other biounit)

Crystal structure of Isocitrate lyase-1 from Candida albicans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: S.107, G.108, W.109, D.124, D.178 Ligands: FMT.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.178, H2O.1, H2O.1, H2O.1, H2O.1 MG.4: 5 residues within 4Å: Chain B: G.108, W.109, D.124, D.178 Ligands: FMT.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.178, H2O.2, H2O.2, H2O.2 MG.7: 7 residues within 4Å: Chain C: Y.105, S.107, G.108, W.109, D.124, D.178 Ligands: FMT.8 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.178, H2O.3, H2O.3, H2O.3, H2O.4 MG.10: 5 residues within 4Å: Chain D: G.108, W.109, D.124, D.178 Ligands: FMT.11 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.178, H2O.5, H2O.6, H2O.6

8 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 6 residues within 4Å: Chain A: C.216, G.217, R.253, E.408 Ligands: MG.1, FMT.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.217, A:R.253, A:R.253, A:N.436 FMT.3: 7 residues within 4Å: Chain A: C.216, H.218, N.436, S.438, S.440, T.470 Ligands: FMT.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.436, A:S.438, A:S.440, A:T.470 FMT.5: 10 residues within 4Å: Chain B: Y.105, D.178, C.216, G.217, R.253, W.406, E.408, N.436 Ligands: MG.4, FMT.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.217, B:R.253, B:R.253, B:E.408 Water bridges: B:G.108 FMT.6: 7 residues within 4Å: Chain B: C.216, H.218, N.436, S.438, S.440, T.470 Ligands: FMT.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.436, B:N.436, B:S.438, B:S.440 FMT.8: 8 residues within 4Å: Chain C: D.124, C.216, R.253, W.406, E.408, N.436 Ligands: MG.7, FMT.9 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.124, C:R.253, C:R.253, C:N.436 FMT.9: 7 residues within 4Å: Chain C: C.216, H.218, N.436, S.438, S.440, T.470 Ligands: FMT.8 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.436, C:N.436, C:S.438, C:S.440, C:T.470 FMT.11: 8 residues within 4Å: Chain D: C.216, G.217, R.253, E.408, N.436, T.470 Ligands: MG.10, FMT.12 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Y.105, D:G.217, D:R.253, D:R.253, D:E.408, D:N.436 Water bridges: D:G.108 FMT.12: 7 residues within 4Å: Chain D: C.216, H.218, N.436, S.438, S.440, T.470 Ligands: FMT.11 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:H.218, D:N.436, D:S.438, D:S.440, D:T.470, D:T.470

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hiragi, K. et al., Structural insights into the targeting specificity of ubiquitin ligase for S. cerevisiae isocitrate lyase but not C. albicans isocitrate lyase. J.Struct.Biol. (2021)

Release Date

2021-06-23

Peptides

Isocitrate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isocitrate lyase

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