MolNFT v1 · #125441 · protein

The crystal structure of substrate-free CYP109E1 from bacillus megaterium at 2.55 ångström resolution

5L90 · Cytochrome P450: “The crystal structure of substrate-free CYP109E1 from bacillus megaterium at 2.55 ångström resolution”. X-ray diffraction, 1 ligand (HEM), 7 pockets (best druggability 0.82). MolNFT v1 #125441 on GenesisL1: 3D…

PDB: 5L90
Type: protein
Length: 770 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome P450
EC: 1.14.14.-
UniProt: D5DKI8
Ligands: HEM
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cytochrome P450 (EC 1.14.14.-)	protein	385	52% helix, 11% strand	D5DKI8

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1150	0.82	0.83	98	empty
2	671	0.77	0.82	59	HEM
3	667	0.76	0.81	61	HEM
4	218	0.51	0.76	23	empty
5	145	0.46	0.77	19	empty

Interfaces

1 interface between chains.

A–B · 792 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5L90 · The crystal structure of substrate-free CYP109E1 from Bacillus megaterium at 2.55… · the same entry in another collection · 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 D5DKI8
Elsewhere: RCSB PDB 5L90 · PDBe 5L90 · UniProt D5DKI8

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