MolNFT v1 · #27523 · protein

X-ray structure of glyoxalase II from arabidopsis thaliana gene AT2G31350

1XM8: “X-ray structure of glyoxalase II from arabidopsis thaliana gene AT2G31350”. X-ray diffraction, 2 ligands (ZN, FE), 2 pockets (best druggability 0.84). MolNFT v1 #27523 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1XM8
Type: protein
Length: 508 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glyoxalase II
EC: 3.1.2.6
Ligands: ZN, FE
Pockets: 2 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glyoxalase II (EC 3.1.2.6)	protein	254	39% helix, 25% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
FE · Fe (III) ion · metal · 2 copies · chains A, B
ACY · Acetic acid · additive · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1002	0.84	0.85	77	ACY
2	149	0.42	0.74	19	empty

Interfaces

1 interface between chains.

A–B · 757 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1XM8 · X-ray structure of glyoxalase II from arabidopsis thaliana gene AT2G31350 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 1XM8 · PDBe 1XM8

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