MolNFT v1 · #22236 · protein

L230A mutant flavocytochrome B2 with benzoylformate

1SZE · Cytochrome B2, mitochondrial: “L230A mutant flavocytochrome B2 with benzoylformate”. X-ray diffraction, 2 ligands (FMN, 173), 14 pockets (best druggability 0.73). MolNFT v1 #22236 on GenesisL1: 3D structure, binding sites and…

PDB: 1SZE
Type: protein
Length: 781 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome B2, mitochondrial
EC: 1.1.2.3
UniProt: P00175
Ligands: FMN, 173
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytochrome B2, mitochondrial (EC 1.1.2.3)	protein	392	42% helix, 13% strand	P00175
B	Cytochrome B2, mitochondrial (EC 1.1.2.3)	protein	389	43% helix, 12% strand	P00175

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
173 · Benzoyl-formic acid · ligand · 2 copies · chains A, B

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

Pockets

14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	211	0.73	0.89	35	FMN, 173
2	242	0.70	0.86	42	FMN, 173
3	60	0.51	0.86	14	empty
4	71	0.47	0.83	14	empty
5	91	0.47	0.80	20	empty

Interfaces

1 interface between chains.

A–B · 2719 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

1SZE · L230A mutant flavocytochrome b2 with benzoylformate · the same entry in another collection · chain A against A, TM-score 1.00
P00175 · AlphaFold monomer V2.0 prediction for cytochrome B2, mitochondrial (P00175) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P00175
Elsewhere: RCSB PDB 1SZE · PDBe 1SZE · UniProt P00175

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