Research workbench

A198G:L230A mutant flavocytochrome B2 with pyruvate bound

Analyse A198G:L230A mutant flavocytochrome B2 with pyruvate bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SZF
Type: protein
Length: 784 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, PYR
Pockets: 12 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytochrome B2, mitochondrial (EC 1.1.2.3)	protein	395	43% helix, 13% strand	P00175
B	Cytochrome B2, mitochondrial (EC 1.1.2.3)	protein	389	42% helix, 13% strand	P00175

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
PYR · Pyruvic acid · ligand · 2 copies · chains A, B

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

Pockets

12 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	342	0.71	0.84	59	FMN, PYR
2	257	0.70	0.85	41	FMN, PYR
3	55	0.50	0.86	15	empty
4	83	0.48	0.82	17	empty
5	110	0.48	0.79	19	empty

Interfaces

1 interface between chains.

A–B · 2707 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

1SZF · A198G:L230A mutant flavocytochrome b2 with pyruvate bound · 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 B 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 1SZF · PDBe 1SZF · UniProt P00175

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