Research workbench

Yeast coproporphyrinogen oxidase

Analyse Yeast coproporphyrinogen oxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1TLB
Type: protein
Length: 1,956 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coproporphyrinogen III oxidase
EC: 1.3.3.3
UniProt: P11353
Ligands: SO4
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, Q, S, U, W	Coproporphyrinogen III oxidase (EC 1.3.3.3)	protein	326	40% helix, 25% strand	P11353

Ligands and binding sites

SO4 · Sulfate ion · ion · chains S

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	311	0.86	0.97	49	empty
2	295	0.85	0.96	46	empty
3	315	0.85	0.96	49	empty
4	284	0.85	0.96	47	empty
5	303	0.84	0.95	48	empty

Interfaces

7 interfaces between chains.

U–W · 1411 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1389 Å² buried · 23 hydrogen bonds · protein-protein
Q–S · 1346 Å² buried · 22 hydrogen bonds · protein-protein
S–U · 900 Å² buried · 13 hydrogen bonds · protein-protein
A–Q · 321 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1TLB · Yeast coproporphyrinogen oxidase · the same entry in another collection · chain S against S, TM-score 1.00
P11353 · AlphaFold monomer V2.0 prediction for oxygen-dependent coproporphyrinogen-III oxidase… · a predicted model of the same protein · chain A against A, TM-score 0.90

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 P11353
Elsewhere: RCSB PDB 1TLB · PDBe 1TLB · UniProt P11353

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