MolNFT v1 · #54977 · protein

Crystal structure of lacy in complex with an affinity inactivator

2Y5Y · Lactose permease: “Crystal structure of lacy in complex with an affinity inactivator”. X-ray diffraction, 2 ligands (TGA, BA), 5 pockets (best druggability 0.85). MolNFT v1 #54977 on GenesisL1: 3D structure, binding sites and…

PDB: 2Y5Y
Type: protein
Length: 780 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lactose permease
UniProt: P02920
Ligands: TGA, BA
Pockets: 5 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 85% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lactose permease	protein	386	86% helix, 0% strand	P02920
B	Lactose permease	protein	394	84% helix, 0% strand	P02920

Ligands and binding sites

TGA · 2-sulfanylethyl beta-D-galactopyranoside · ligand · 2 copies · chains A, B
BA · Barium ion · metal · 2 copies · chains A, B

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	1105	0.85	0.86	80	TGA
2	1050	0.85	0.85	72	BA, TGA
3	616	0.72	0.79	56	empty
4	70	0.40	0.79	17	empty
5	101	0.38	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 449 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

2Y5Y · Crystal structure of LacY in complex with an affinity inactivator · the same entry in another collection · chain A against A, TM-score 1.00
P02920 · AlphaFold monomer V2.0 prediction for lactose permease (P02920) · 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 P02920
Elsewhere: RCSB PDB 2Y5Y · PDBe 2Y5Y · UniProt P02920

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