MolNFT v1 · #19404 · protein

Flavocytochrome C3 from shewanella frigidimarina

1QJD: “Flavocytochrome C3 from shewanella frigidimarina”. X-ray diffraction, 4 ligands (HEC, FAD, TEO), 6 pockets (best druggability 0.85). MolNFT v1 #19404 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1QJD
Type: protein
Length: 568 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Flavocytochrome C3
UniProt: Q02469
Ligands: HEC, FAD, TEO, NA
Pockets: 6 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Flavocytochrome C3	protein	568	36% helix, 19% strand	Q02469

Ligands and binding sites

HEC · Heme C · ligand · 4 copies · chains A
FAD · Flavin-adenine dinucleotide · ligand · chains A
TEO · Malate like intermediate · ligand · chains A
NA · Sodium ion · metal · chains A
GOL · Glycerol · additive · chains A

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1147	0.85	0.86	151	HEC, FAD, TEO
2	280	0.61	0.79	28	empty
3	91	0.37	0.75	19	empty
4	80	0.37	0.77	16	empty
5	84	0.31	0.73	13	empty

Modifications

Observed in the structure: 8 cofactor (heme c attachment).

Compared structures

1QJD · Flavocytochrome C3 from Shewanella frigidimarina · 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 Q02469
Elsewhere: RCSB PDB 1QJD · PDBe 1QJD · UniProt Q02469

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