MolNFT v1 · #90905 · protein

Crystal structure of uroporphyrinogen decarboxylase (upd) from burkholderia thailandensis E264

4EXQ: “Crystal structure of uroporphyrinogen decarboxylase (upd) from burkholderia thailandensis E264”. X-ray diffraction, 1 ligand (NA), 2 pockets (best druggability 0.72). MolNFT v1 #90905 on GenesisL1: 3D structure, binding sites and…

PDB: 4EXQ
Type: protein
Length: 357 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uroporphyrinogen decarboxylase
EC: 4.1.1.37
UniProt: Q2STF3
Ligands: NA
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uroporphyrinogen decarboxylase (EC 4.1.1.37)	protein	357	51% helix, 13% strand	Q2STF3

Ligands and binding sites

NA · Sodium ion · metal · 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	454	0.72	0.81	37	empty
2	111	0.47	0.80	24	empty

Compared structures

4EXQ · CRYSTAL STRUCTURE of UROPORPHYRINOGEN DECARBOXYLASE (UPD) FROM BURKHOLDERIA THAILANDENSIS… · the same entry in another collection · chain A against A, TM-score 1.00
Q2STF3 · AlphaFold monomer V2.0 prediction for uroporphyrinogen decarboxylase (Q2STF3) · 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 Q2STF3
Elsewhere: RCSB PDB 4EXQ · PDBe 4EXQ · UniProt Q2STF3

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