MolNFT v1 · #125194 · protein

X-ray structure of the substrate-free cytochrome P450 pntm

5L1R · Pentalenolactone synthase: “X-ray structure of the substrate-free cytochrome P450 pntm”. X-ray diffraction, 2 ligands (HEM, BCN), 2 pockets (best druggability 0.85). MolNFT v1 #125194 on GenesisL1: 3D structure, binding sites and…

PDB: 5L1R
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, BCN
Pockets: 2 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pentalenolactone synthase (EC 1.14.19.8)	protein	397	53% helix, 11% strand	E3VWI3

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains A
BCN · Bicine · 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	913	0.85	0.86	87	HEM, BCN
2	80	0.43	0.80	15	empty

Compared structures

5L1R · X-ray Structure of the Substrate-free Cytochrome P450 PntM · 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 5L1R · PDBe 5L1R · UniProt E3VWI3

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