MolNFT v1 · #19016 · protein

Hypothetical protein yfdw from E. COLI bound to coenzyme a

1Q6Y: “Hypothetical protein yfdw from E. COLI bound to coenzyme a”. X-ray diffraction, 1 ligand (COA), 5 pockets (best druggability 0.63). MolNFT v1 #19016 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1Q6Y
Type: protein
Length: 417 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein yfdw
UniProt: P69902
Ligands: COA
Pockets: 5 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein yfdw	protein	417	41% helix, 13% strand	P69902

Ligands and binding sites

COA · Coenzyme A · ligand · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains A

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

Pockets

5 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	252	0.63	0.81	39	COA
2	149	0.52	0.80	41	empty
3	126	0.51	0.80	17	MPD
4	131	0.46	0.78	24	empty
5	116	0.42	0.76	16	empty

Compared structures

1Q6Y · Hypothetical protein YfdW from E. coli bound to Coenzyme A · the same entry in another collection · chain A against A, TM-score 1.00
P69902 · AlphaFold monomer V2.0 prediction for formyl-COA:OXALATE CoA- transferase (P69902) · a predicted model of the same protein · chain A 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 P69902
Elsewhere: RCSB PDB 1Q6Y · PDBe 1Q6Y · UniProt P69902

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