MolNFT v1 · #63415 · protein

Desulfovibrio desulfuricans (atcc 29577) semiquinone flavodoxin

3F90: “Desulfovibrio desulfuricans (atcc 29577) semiquinone flavodoxin”. X-ray diffraction, 1 ligand (FMN), 10 pockets (best druggability 0.67). MolNFT v1 #63415 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3F90
Type: protein
Length: 1,176 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Flavodoxin
UniProt: P26492
Ligands: FMN
Pockets: 10 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, F, H, I, G	Flavodoxin	protein	147	36% helix, 22% strand	P26492

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 8 copies · chains A, G, B, D, E, F, H, I

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

Pockets

10 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	616	0.67	0.77	61	FMN
2	549	0.67	0.77	59	FMN
3	474	0.67	0.79	55	FMN
4	284	0.54	0.75	33	empty
5	88	0.48	0.82	24	FMN

Interfaces

5 interfaces between chains.

D–E · 607 Å² buried · 14 hydrogen bonds · protein-protein
A–F · 549 Å² buried · 16 hydrogen bonds · protein-protein
B–E · 360 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 357 Å² buried · 6 hydrogen bonds · protein-protein
A–G · 354 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3F90 · Desulfovibrio desulfuricans (ATCC 29577) semiqui flavodoxin · the same entry in another collection · chain G against G, TM-score 1.00
P26492 · AlphaFold monomer V2.0 prediction for flavodoxin (P26492) · a predicted model of the same protein · chain D 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 P26492
Elsewhere: RCSB PDB 3F90 · PDBe 3F90 · UniProt P26492

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