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X-ray structure of cytochrome P450 pntm with pentalenolactone

Analyse X-ray structure of cytochrome P450 pntm with pentalenolactone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5L1P
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, 7PT
Pockets: 2 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pentalenolactone synthase (EC 1.14.19.8)	protein	397	53% helix, 10% strand	E3VWI3

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains A
7PT · pentalenolactone · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	981	0.86	0.86	89	HEM, 7PT
2	68	0.41	0.81	15	empty

Compared structures

5L1P · X-ray Structure of Cytochrome P450 PntM with Pentalenolactone · 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 5L1P · PDBe 5L1P · UniProt E3VWI3

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