MolNFT v1 · #66968 · protein
Crystal structure of ppo from bacillus subtilis with af
3I6D · Protoporphyrinogen oxidase: “Crystal structure of ppo from bacillus subtilis with af”. X-ray diffraction, 3 ligands (FAD, ACJ, PO4), 5 pockets (best druggability 0.83). MolNFT v1 #66968 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3I6D
- Type
- protein
- Length
- 833 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protoporphyrinogen oxidase
- EC
- 1.3.3.4
- UniProt
- P32397
- Ligands
- FAD, ACJ, PO4
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protoporphyrinogen oxidase (EC 1.3.3.4) | protein | 414 | 34% helix, 25% strand | P32397 |
| B | Protoporphyrinogen oxidase (EC 1.3.3.4) | protein | 419 | 34% helix, 24% strand | P32397 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- ACJ · 5-[2-chloro-4-(trifluoromethyl)phenoxy]-2-nitrobenzoic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.83 | 0.87 | 86 | FAD, ACJ |
| 2 | 699 | 0.83 | 0.87 | 95 | FAD, ACJ |
| 3 | 50 | 0.46 | 0.86 | 17 | empty |
| 4 | 52 | 0.36 | 0.79 | 12 | empty |
| 5 | 69 | 0.35 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 564 Ų buried · 3 hydrogen bonds · protein-protein
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 P32397
- Elsewhere: RCSB PDB 3I6D · PDBe 3I6D · UniProt P32397
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