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Structure of YhdA, K109L variant

Analyse Structure of YhdA, K109L variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GFQ
Type: protein
Length: 669 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.996
Source: Bacillus subtilis
Molecule: FMN-dependent NADPH-azoreductase
EC: 1.7.-.-
UniProt: O07529
Ligands: FMN
Pockets: 6 · best druggability 0.67

Structure

x-ray diffraction · resolution 2.996 · 2 distinct chains · 45% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	FMN-dependent NADPH-azoreductase (EC 1.7.-.-)	protein	168	45% helix, 19% strand	O07529
B, C, D	FMN-dependent NADPH-azoreductase (EC 1.7.-.-)	protein	167	45% helix, 20% strand	O07529

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

6 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	334	0.67	0.81	51	FMN
2	52	0.65	0.96	12	empty
3	183	0.60	0.82	27	empty
4	137	0.49	0.79	17	empty
5	128	0.37	0.73	21	FMN

Interfaces

5 interfaces between chains.

A–B · 1149 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1125 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 750 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 454 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 284 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3GFQ · Structure of yhda, K109L variant · the same entry in another collection · chain D against D, TM-score 1.00
O07529 · AlphaFold monomer V2.0 prediction for FMN-dependent NADPH- azoreductase (O07529) · 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 O07529
Elsewhere: RCSB PDB 3GFQ · PDBe 3GFQ · UniProt O07529

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