MolNFT v1 · #63337 · protein

Desulfovibrio desulfuricans (atcc 29577) oxidized flavodoxin

3F6R: “Desulfovibrio desulfuricans (atcc 29577) oxidized flavodoxin”. X-ray diffraction, 1 ligand (FMN), 10 pockets (best druggability 0.52). MolNFT v1 #63337 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3F6R
Type: protein
Length: 588 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Flavodoxin
UniProt: P26492
Ligands: FMN
Pockets: 10 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Flavodoxin	protein	147	35% helix, 26% strand	P26492

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D

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

Pockets

10 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	170	0.52	0.79	22	empty
2	159	0.49	0.77	20	empty
3	111	0.49	0.81	25	FMN
4	111	0.45	0.79	22	FMN
5	117	0.45	0.78	23	FMN

Interfaces

3 interfaces between chains.

A–B · 630 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 556 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 268 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3F6R · Desulfovibrio desulfuricans (ATCC 29577) oxidized flavodoxin · the same entry in another collection · chain D against D, TM-score 1.00
P26492 · AlphaFold monomer V2.0 prediction for flavodoxin (P26492) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P26492
Elsewhere: RCSB PDB 3F6R · PDBe 3F6R · UniProt P26492

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