MolNFT v1 · #5466 · protein

Structure of orotidine 5'-monophosphate decarboxylase from E. COLI, co-crystallised with the inhibitor bmp

1EIX: “Structure of orotidine 5'-monophosphate decarboxylase from E. COLI, co-crystallised with the inhibitor bmp”. X-ray diffraction, 1 ligand (BMQ), 7 pockets (best druggability 0.76). MolNFT v1 #5466 on GenesisL1: 3D structure, binding…

PDB: 1EIX
Type: protein
Length: 925 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Orotidine 5'-monophosphate decarboxylase
EC: 4.1.1.23
UniProt: P08244
Ligands: BMQ
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Orotidine 5'-monophosphate decarboxylase (EC 4.1.1.23)	protein	231	47% helix, 17% strand	P08244
C	Orotidine 5'-monophosphate decarboxylase (EC 4.1.1.23)	protein	232	50% helix, 17% strand	P08244

Ligands and binding sites

BMQ · 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	100	0.76	0.97	27	BMQ
2	94	0.75	0.97	27	BMQ
3	126	0.74	0.94	33	BMQ
4	54	0.71	0.98	24	empty
5	122	0.71	0.92	33	BMQ

Interfaces

3 interfaces between chains.

A–B · 2190 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 2163 Å² buried · 34 hydrogen bonds · protein-protein
B–D · 117 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1EIX · Structure of orotidine 5'-monophosphate decarboxylase from E. COLI, co-crystallised with… · the same entry in another collection · chain A against A, TM-score 1.00
P08244 · AlphaFold monomer V2.0 prediction for orotidine 5'-phosphate decarboxylase (P08244) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 P08244
Elsewhere: RCSB PDB 1EIX · PDBe 1EIX · UniProt P08244

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