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Crystal structure of oxalate decarboxylase formate complex

Analyse Crystal structure of oxalate decarboxylase formate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1L3J
Type: protein
Length: 372 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yvrk protein
UniProt: O34714
Ligands: MN, MG
Pockets: 3 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yvrk protein	protein	372	16% helix, 39% strand	O34714

Ligands and binding sites

MN · Manganese (II) ion · metal · 2 copies · chains A
MG · Magnesium ion · metal · chains A
FMT · Formic acid · additive · 2 copies · chains A

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

Pockets

3 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	128	0.54	0.82	22	FMT
2	77	0.33	0.74	16	empty
3	57	0.29	0.74	16	empty

Compared structures

1L3J · Crystal Structure of Oxalate Decarboxylase Formate Complex · the same entry in another collection · chain A against A, TM-score 1.00
O34714 · AlphaFold monomer V2.0 prediction for oxalate decarboxylase oxdc (O34714) · 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 O34714
Elsewhere: RCSB PDB 1L3J · PDBe 1L3J · UniProt O34714

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