Research workbench
Native-sad phasing for thit from listeria monocytogenes serovar.
Analyse Native-sad phasing for thit from listeria monocytogenes serovar. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TKR
- Type
- protein
- Length
- 369 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiamine transporter thia
- UniProt
- S5L6I0
- Ligands
- BGL, TPP
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamine transporter thia | protein | 183 | 78% helix, 1% strand | S5L6I0 |
| B | Thiamine transporter thia | protein | 186 | 76% helix, 1% strand | S5L6I0 |
Ligands and binding sites
- BGL · 2-O-octyl-beta-D-glucopyranose · ligand · 15 copies · chains A, B
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.79 | 0.91 | 35 | TPP |
| 2 | 314 | 0.74 | 0.87 | 33 | TPP |
| 3 | 51 | 0.27 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1095 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4TKR · Native-SAD phasing for ThiT from Listeria monocytogenes serovar. · the same entry in another collection · chain A against A, TM-score 1.00
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 S5L6I0
- Elsewhere: RCSB PDB 4TKR · PDBe 4TKR · UniProt S5L6I0
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