Research workbench
X-ray structure of 2-mercaptoethanol modified M81C mutant of cytochrome P450 pntm with pentalenolactone F
Analyse X-ray structure of 2-mercaptoethanol modified M81C mutant of cytochrome P450… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L1W
- 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
- 7PF, HEM
- Pockets
- 5 · 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
- 7PF · pentalenolactone F · ligand · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
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 | 549 | 0.85 | 0.91 | 59 | 7PF, HEM |
| 2 | 383 | 0.67 | 0.80 | 38 | empty |
| 3 | 83 | 0.44 | 0.80 | 15 | empty |
| 4 | 52 | 0.41 | 0.82 | 13 | empty |
| 5 | 55 | 0.29 | 0.74 | 14 | empty |
Modifications
Observed in the structure: 1 modified (artifact).
Compared structures
- 5L1W · X-ray Structure of 2-Mercaptoethanol modified M81C mutant of Cytochrome P450 PntM with… · 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 5L1W · PDBe 5L1W · UniProt E3VWI3
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