MolNFT v1 · #6354 · protein

Crystal structure of the NI(II)-bound glyoxalase I from escherichia COLI

1F9Z: “Crystal structure of the NI(II)-bound glyoxalase I from escherichia COLI”. X-ray diffraction, 1 ligand (NI), 2 pockets (best druggability 0.49). MolNFT v1 #6354 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1F9Z
Type: protein
Length: 256 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glyoxalase I
EC: 4.4.1.5
UniProt: P0AC81
Ligands: NI
Pockets: 2 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glyoxalase I (EC 4.4.1.5)	protein	128	16% helix, 44% strand	P0AC81

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	223	0.49	0.74	28	empty
2	179	0.43	0.73	26	empty

Interfaces

1 interface between chains.

A–B · 1734 Å² buried · 47 hydrogen bonds · protein-protein

Compared structures

1F9Z · Crystal structure of the NI(II)-bound glyoxalase I from escherichia COLI · the same entry in another collection · chain A against A, TM-score 1.00
P0AC81 · AlphaFold monomer V2.0 prediction for lactoylglutathione lyase (P0AC81) · a predicted model of the same protein · chain A against A, TM-score 0.90

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 P0AC81
Elsewhere: RCSB PDB 1F9Z · PDBe 1F9Z · UniProt P0AC81

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