MolNFT v1 · #63363 · protein

B.SUBTILIS yvgn

3F7J · Yvgn protein: “B.SUBTILIS yvgn”. X-ray diffraction, 2 ligands (K, NO3), 6 pockets (best druggability 0.80). MolNFT v1 #63363 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3F7J
Type: protein
Length: 552 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yvgn protein
UniProt: O32210
Ligands: K, NO3
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Yvgn protein	protein	276	43% helix, 17% strand	O32210

Ligands and binding sites

K · Potassium ion · metal · 2 copies · chains A, B
NO3 · Nitrate ion · ion · 9 copies · chains A, B

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	538	0.80	0.86	74	NO3, K
2	172	0.56	0.81	31	NO3
3	83	0.41	0.79	20	NO3
4	98	0.40	0.76	20	NO3
5	73	0.33	0.75	17	empty

Interfaces

1 interface between chains.

A–B · 866 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

3F7J · B.subtilis YvgN · the same entry in another collection · chain B against B, TM-score 1.00
O32210 · AlphaFold monomer V2.0 prediction for glyoxal reductase (O32210) · a predicted model of the same protein · 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 O32210
Elsewhere: RCSB PDB 3F7J · PDBe 3F7J · UniProt O32210

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