SMTL ID : 7wsz.1

human glyoxalase I (with C-ter His tag) in glycerol-bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.127, E.173 Chain B: Q.34, E.100 Ligands: GOL.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.127, A:E.173, B:E.100 ZN.10: 4 residues within 4Å: Chain A: Q.34, E.100 Chain B: H.127, E.173 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.127, B:E.173, A:E.100, H2O.2, H2O.6

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: H.127, M.158, E.173, M.184 Chain B: Q.34, L.70, E.100 Ligands: ZN.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.34, B:Q.34 GOL.3: 7 residues within 4Å: Chain A: A.131, V.132, P.133, P.177 Chain B: D.29, L.31, S.94 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.132, B:D.29 GOL.4: 6 residues within 4Å: Chain A: L.57, I.58, Q.59, K.60, K.88 Chain B: L.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.58, A:K.60, A:K.88 Water bridges: A:K.60 GOL.11: 5 residues within 4Å: Chain B: L.57, I.58, Q.59, K.60, K.88 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.58, B:K.60, B:K.88 Water bridges: B:K.60

3 x BO3: BORIC ACID(Non-covalent)

BO3.5: 4 residues within 4Å: Chain A: T.56, L.57 Chain B: C.20, D.22 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.57 Water bridges: A:T.56, B:A.23 BO3.6: 3 residues within 4Å: Chain A: R.38, N.104 Chain B: R.123 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.38, A:R.38, A:N.104, A:N.104, B:R.123, B:R.123 BO3.12: 4 residues within 4Å: Chain A: R.123 Chain B: R.38, T.102, N.104 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.123, A:R.123, B:R.38, B:N.104, B:N.104

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 4 residues within 4Å: Chain A: T.27, K.28, F.30 Chain B: Y.75 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:G.54, B:G.54, B:E.76, A:T.27

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

BME.8: 4 residues within 4Å: Chain A: E.76, R.95 Chain B: K.96 Ligands: BME.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.95 Water bridges: A:E.76, A:E.76, A:W.91 BME.9: 4 residues within 4Å: Chain A: S.94, R.95, K.96 Ligands: BME.8 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.96 Water bridges: B:K.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Usami, M. et al., Crystal structures of human glyoxalase I and its complex with TLSC702 reveal inhibitor binding mode and substrate preference. Febs Lett. (2022)

Release Date

2022-04-13

Peptides

Lactoylglutathione lyase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lactoylglutathione lyase

Related Entries With Identical Sequence