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ThiT with LMG135 bound

Analyse ThiT with LMG135 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4POV
Type: protein
Length: 354 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.2
Source: Lactococcus lactis subsp. cremoris
Molecule: Thiamine transporter ThiT
UniProt: A2RI47
Ligands: 2VY, BNG, CL
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · resolution 2.2 · 2 distinct chains · 75% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thiamine transporter ThiT	protein	178	75% helix, 3% strand	A2RI47
B	Thiamine transporter ThiT	protein	176	74% helix, 3% strand	A2RI47

Ligands and binding sites

2VY · 4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophene-2-carbaldehyde · ligand · 2 copies · chains A, B
BNG · nonyl beta-D-glucopyranoside · sugar · 6 copies · chains A, B
CL · Chloride ion · ion · chains B
PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, B
PG4 · Tetraethylene glycol · additive · 9 copies · chains A, B
1PE · Pentaethylene glycol · additive · 3 copies · chains A, B
PGE · Triethylene glycol · additive · 3 copies · chains A, B
PG0 · 2-(2-methoxyethoxy)ethanol · additive · 2 copies · chains A, B
P6G · Hexaethylene glycol · additive

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	0.89	30	2VY, PG4
2	219	0.70	0.86	33	2VY, PG0
3	320	0.68	0.81	30	PG4, 1PE
4	113	0.39	0.74	18	PEG

Interfaces

1 interface between chains.

A–B · 617 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4POV · Thit with LMG135 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 4POV · PDBe 4POV · UniProt A2RI47

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