MolNFT v1 · #6934 · protein

Human glyoxalase I with benzyl-glutathione inhibitor

1FRO · Lactoylglutathione lyase: “Human glyoxalase I with benzyl-glutathione inhibitor”. X-ray diffraction, 2 ligands (GSB, ZN), 8 pockets (best druggability 0.79). MolNFT v1 #6934 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1FRO
Type: protein
Length: 704 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lactoylglutathione lyase
EC: 4.4.1.5
UniProt: Q04760
Ligands: GSB, ZN
Pockets: 8 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Lactoylglutathione lyase (EC 4.4.1.5)	protein	176	27% helix, 28% strand	Q04760

Ligands and binding sites

GSB · S-benzyl-glutathione · ligand · 4 copies · chains A, B, D, C
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	966	0.79	0.80	83	GSB
2	1089	0.77	0.79	80	GSB
3	213	0.64	0.82	29	GSB
4	230	0.64	0.82	32	GSB
5	140	0.42	0.75	28	empty

Interfaces

5 interfaces between chains.

C–D · 3730 Å² buried · 46 hydrogen bonds · protein-protein
A–B · 3722 Å² buried · 44 hydrogen bonds · protein-protein
B–D · 240 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 150 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 85 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1FRO · Human glyoxalase I with benzyl-glutathione inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
Q04760 · AlphaFold monomer V2.0 prediction for lactoylglutathione lyase (Q04760) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q04760
Elsewhere: RCSB PDB 1FRO · PDBe 1FRO · UniProt Q04760

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