MolNFT v1 · #21574 · protein
Crystal structure of protoporphyrinogen IX oxidase
1SEZ · Protoporphyrinogen oxidase, mitochondrial: “Crystal structure of protoporphyrinogen IX oxidase”. X-ray diffraction, 3 ligands (FAD, OMN, TON), 5 pockets (best druggability 0.83). MolNFT v1 #21574 on GenesisL1: 3D structure, binding…
- PDB
- 1SEZ
- Type
- protein
- Length
- 930 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protoporphyrinogen oxidase, mitochondrial
- EC
- 1.3.3.4
- UniProt
- O24164
- Ligands
- FAD, OMN, TON
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protoporphyrinogen oxidase, mitochondrial (EC 1.3.3.4) | protein | 465 | 37% helix, 22% strand | O24164 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- OMN · 4-bromo-3-(5'-carboxy-4'-chloro-2'-fluorophenyl)-1-methyl-5-trifluoromethyl-pyrazol · ligand · 2 copies · chains A, B
- TON · 2-{2-[4-(1,1,3,3-tetramethylbutyl) phenoxy]ethoxy}ethanol · ligand · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.83 | 0.87 | 78 | FAD, OMN |
| 2 | 874 | 0.83 | 0.85 | 87 | FAD, OMN |
| 3 | 407 | 0.77 | 0.85 | 49 | TON |
| 4 | 129 | 0.64 | 0.87 | 22 | empty |
| 5 | 82 | 0.51 | 0.83 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 718 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 1SEZ · Crystal Structure of Protoporphyrinogen IX Oxidase · the same entry in another collection · chain A against A, TM-score 1.00
- O24164 · AlphaFold monomer V2.0 prediction for protoporphyrinogen oxidase, mitochondrial (O24164) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O24164
- Elsewhere: RCSB PDB 1SEZ · PDBe 1SEZ · UniProt O24164
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