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Crystal structure of oxalate decarboxylase

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

PDB: 1UW8
Type: protein
Length: 377 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oxalate decarboxylase oxdc
EC: 4.1.1.2
UniProt: O34714
Ligands: MN
Pockets: 4 · best druggability 0.30

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oxalate decarboxylase oxdc (EC 4.1.1.2)	protein	377	15% helix, 40% strand	O34714

Ligands and binding sites

MN · Manganese (II) ion · metal · 2 copies · chains A
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

4 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	59	0.30	0.75	16	empty
2	59	0.29	0.73	10	empty
3	50	0.26	0.74	11	empty
4	53	0.26	0.73	16	empty

Compared structures

1UW8 · Crystal structure of oxalate decarboxylase · 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 1UW8 · PDBe 1UW8 · UniProt O34714

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