MolNFT v1 · #62578 · protein

Coproporphyrinogen III oxidase from leishmania donovani

3EJO: “Coproporphyrinogen III oxidase from leishmania donovani”. X-ray diffraction, 6 pockets (best druggability 0.79). MolNFT v1 #62578 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3EJO
Type: protein
Length: 583 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coproporphyrinogen III oxidase
EC: 1.3.3.3
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coproporphyrinogen III oxidase (EC 1.3.3.3)	protein	292	45% helix, 26% strand	—
B	Coproporphyrinogen III oxidase (EC 1.3.3.3)	protein	291	46% helix, 27% strand	—

Ligands and binding sites

ACT · Acetate ion · additive · 2 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	528	0.79	0.86	56	ACT
2	687	0.78	0.83	53	ACT
3	83	0.35	0.75	19	empty
4	77	0.32	0.74	23	empty
5	79	0.32	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 1399 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

3EJO · Coproporphyrinogen III oxidase from Leishmania donovani · 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
Elsewhere: RCSB PDB 3EJO · PDBe 3EJO

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