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Crystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate

Analyse Crystal structure of the mutant L123S of orotidine 5'-monophosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PBY
Type: protein
Length: 437 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Orotidine 5'-monophosphate decarboxylase
EC: 4.1.1.23
UniProt: O26232
Ligands: UP6
Pockets: 1 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Orotidine 5'-monophosphate decarboxylase (EC 4.1.1.23)	protein	219	50% helix, 19% strand	O26232
B	Orotidine 5'-monophosphate decarboxylase (EC 4.1.1.23)	protein	218	50% helix, 19% strand	O26232

Ligands and binding sites

UP6 · 6-aza uridine 5'-monophosphate · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	303	0.85	0.95	78	UP6

Interfaces

1 interface between chains.

A–B · 1757 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

3PBY · Crystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from… · 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
Every structure of UniProt O26232
Elsewhere: RCSB PDB 3PBY · PDBe 3PBY · UniProt O26232

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