MolNFT v1 · #125193 · protein
X-ray structure of cytochrome P450 pntm with dihydropentalenolactone F
5L1Q · Pentalenolactone synthase: “X-ray structure of cytochrome P450 pntm with dihydropentalenolactone F”. X-ray diffraction, 2 ligands (HEM, 7DF), 2 pockets (best druggability 0.85). MolNFT v1 #125193 on GenesisL1: 3D structure, binding…
- PDB
- 5L1Q
- Type
- protein
- Length
- 397 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pentalenolactone synthase
- EC
- 1.14.19.8
- UniProt
- E3VWI3
- Ligands
- HEM, 7DF
- Pockets
- 2 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pentalenolactone synthase (EC 1.14.19.8) | protein | 397 | 54% helix, 10% strand | E3VWI3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- 7DF · Dihydropentalenolactone F · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.85 | 0.87 | 78 | HEM, 7DF |
| 2 | 79 | 0.44 | 0.81 | 16 | empty |
Compared structures
- 5L1Q · X-ray Structure of Cytochrome P450 PntM with Dihydropentalenolactone F · the same entry in another collection · chain A against A, TM-score 1.00
- E3VWI3 · AlphaFold monomer V2.0 prediction for pentalenolactone synthase (E3VWI3) · a predicted model of the same protein · 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
- Every structure of UniProt E3VWI3
- Elsewhere: RCSB PDB 5L1Q · PDBe 5L1Q · UniProt E3VWI3
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