SMTL ID : 9fkc.2 (1 other biounit)

Crystal structure of human Glucose-6-phosphate isomerase with citraconate ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x CIZ: (~{Z})-2-methylbut-2-enedioic acid(Non-covalent)

CIZ.1: 11 residues within 4Å: Chain A: I.157, G.158, G.159, S.160, S.210, K.211, T.212, F.213, T.215, T.218 Chain B: H.389 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.160, A:S.210, A:K.211, A:T.212, A:T.212, A:T.215, A:T.215 Water bridges: A:I.157, A:T.218 CIZ.3: 12 residues within 4Å: Chain A: H.389 Chain B: I.157, G.158, G.159, S.160, S.210, K.211, T.212, F.213, T.215, T.218, K.519 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.160, B:S.210, B:S.210, B:K.211, B:T.212, B:T.215, B:T.215

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 17 residues within 4Å: Chain A: R.21, S.22, L.24, L.59, F.331, G.398, T.399, K.400, M.401, N.471, R.472, P.473 Chain B: Y.363, R.370, V.371, D.372, H.373 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.21, A:N.471, B:R.370, B:H.373 Water bridges: A:R.472, A:R.472

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 12 residues within 4Å: Chain B: R.21, S.22, L.24, L.59, F.331, T.399, K.400, M.401, G.470, N.471, R.472, P.473 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.21, B:N.471, B:R.472 Water bridges: B:R.21, B:R.472

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.5: 3 residues within 4Å: Chain B: R.180, V.181, W.182 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jonatansdottir, Y.Y. et al., Human glycolysis isomerases are inhibited by weak metabolite modulators. Febs J. (2025)

Release Date

2025-03-12

Peptides

Glucose-6-phosphate isomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Glucose-6-phosphate isomerase

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