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Coproporphyrinogen III oxidase from leishmania naiffi

Analyse Coproporphyrinogen III oxidase from leishmania naiffi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3E8J
Type: protein
Length: 571 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: 5 · best druggability 0.77

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	285	46% helix, 27% strand	—
B	Coproporphyrinogen III oxidase (EC 1.3.3.3)	protein	286	45% helix, 27% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 5 copies · chains A, B
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

5 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	593	0.77	0.84	51	ACT
2	639	0.76	0.82	52	ACT
3	90	0.38	0.77	26	empty
4	81	0.37	0.77	20	empty
5	55	0.25	0.73	19	empty

Interfaces

1 interface between chains.

A–B · 1356 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

3E8J · Coproporphyrinogen III oxidase from Leishmania naiffi · 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 3E8J · PDBe 3E8J

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