MolNFT v1 · #103710 · protein

Thit with LMG139 bound

4POP · Thiamine transporter thit: “Thit with LMG139 bound”. X-ray diffraction, 2 ligands (BNG, 2VY), 4 pockets (best druggability 0.73). MolNFT v1 #103710 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4POP
Type: protein
Length: 353 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thiamine transporter thit
UniProt: A2RI47
Ligands: BNG, 2VY
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 74% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thiamine transporter thit	protein	177	75% helix, 3% strand	A2RI47
B	Thiamine transporter thit	protein	176	73% helix, 3% strand	A2RI47

Ligands and binding sites

BNG · nonyl beta-D-glucopyranoside · ligand · 5 copies · chains A, B
2VY · 4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophene-2-carbaldehyde · ligand · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 21 copies · chains A, B
PG4 · Tetraethylene glycol · additive · 9 copies · chains A, B
PG0 · 2-(2-methoxyethoxy)ethanol · additive · 3 copies · chains A, B
1PE · Pentaethylene glycol · additive · 3 copies · chains A, B
PGE · Triethylene glycol · additive · chains A
P6G · Hexaethylene glycol · additive · chains A
P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains B

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

Pockets

4 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	215	0.73	0.88	34	2VY, PEG
2	224	0.72	0.87	35	2VY
3	300	0.68	0.82	30	PG0, PG4
4	110	0.39	0.74	17	PEG

Interfaces

1 interface between chains.

A–B · 618 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4POP · ThiT with LMG139 bound · the same entry in another collection · chain A against A, TM-score 1.00
A2RI47 · AlphaFold monomer V2.0 prediction for thiamine transporter thit (A2RI47) · 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 A2RI47
Elsewhere: RCSB PDB 4POP · PDBe 4POP · UniProt A2RI47

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