MolNFT v1 · #104290 · protein

Structure of the E. COLI peptide transporter ybgh

4Q65 · Dipeptide permease D: “Structure of the E. COLI peptide transporter ybgh”. X-ray diffraction, 4 pockets (best druggability 0.77). MolNFT v1 #104290 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Q65
Type: protein
Length: 437 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dipeptide permease D
UniProt: P75742
Pockets: 4 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dipeptide permease D	protein	437	79% helix, 0% strand	P75742

Pockets

4 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	961	0.77	0.79	61	empty
2	281	0.56	0.76	37	empty
3	55	0.48	0.85	17	empty
4	60	0.29	0.74	14	empty

Compared structures

4Q65 · Structure of the E. coli Peptide Transporter YbgH · the same entry in another collection · chain A against A, TM-score 1.00
P75742 · AlphaFold monomer V2.0 prediction for dipeptide permease D (P75742) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P75742
Elsewhere: RCSB PDB 4Q65 · PDBe 4Q65 · UniProt P75742

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