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Periplasmic thiamin binding protein

Analyse Periplasmic thiamin binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QRY
Type: protein
Length: 1,245 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thiamine-binding periplasmic protein
UniProt: P31550
Ligands: TPS
Pockets: 17 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thiamine-binding periplasmic protein	protein	308	43% helix, 21% strand	P31550
B	Thiamine-binding periplasmic protein	protein	309	40% helix, 21% strand	P31550
C	Thiamine-binding periplasmic protein	protein	318	41% helix, 21% strand	P31550
D	Thiamine-binding periplasmic protein	protein	310	41% helix, 21% strand	P31550

Ligands and binding sites

TPS · Thiamin phosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	193	0.73	0.89	36	TPS
2	236	0.72	0.87	38	TPS
3	654	0.72	0.79	54	empty
4	534	0.72	0.81	53	empty
5	182	0.69	0.87	29	TPS

Interfaces

4 interfaces between chains.

A–B · 1292 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1275 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 348 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 294 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 18 modified (engineered).

Compared structures

2QRY · Periplasmic thiamin binding protein · the same entry in another collection · chain D against D, TM-score 1.00
P31550 · AlphaFold monomer V2.0 prediction for thiamine-binding periplasmic protein (P31550) · 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 P31550
Elsewhere: RCSB PDB 2QRY · PDBe 2QRY · UniProt P31550

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