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Structure of human protoporphyrinogen IX oxidase
Analyse Structure of human protoporphyrinogen IX oxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NKS
- Type
- protein
- Length
- 465 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Homo sapiens
- Molecule
- Protoporphyrinogen oxidase
- EC
- 1.3.3.4
- UniProt
- P50336
- Ligands
- ACJ, FAD
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.9 · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protoporphyrinogen oxidase (EC 1.3.3.4) | protein | 465 | 40% helix, 22% strand | P50336 |
Ligands and binding sites
- ACJ · 5-[2-chloro-4-(trifluoromethyl)phenoxy]-2-nitrobenzoic acid · ligand · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.81 | 0.82 | 113 | ACJ, FAD |
| 2 | 101 | 0.45 | 0.80 | 25 | empty |
| 3 | 118 | 0.45 | 0.78 | 22 | empty |
Compared structures
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 P50336
- Elsewhere: RCSB PDB 3NKS · PDBe 3NKS · UniProt P50336
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