MolNFT v1 · #100663 · protein
Structure of thit with av-38 bound
4N4D · Thiamine binding protein thit: “Structure of thit with av-38 bound”. X-ray diffraction, 3 ligands (BNG, XX8, CL), 4 pockets (best druggability 0.76). MolNFT v1 #100663 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4N4D
- Type
- protein
- Length
- 352 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiamine binding protein thit
- UniProt
- D8KFM5
- Ligands
- BNG, XX8, CL
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thiamine binding protein thit | protein | 176 | 74% helix, 3% strand | D8KFM5 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 5 copies · chains A, B
- XX8 · {3-[(4-amino-2-methylpyrimidin-5-yl)methyl]phenyl}methanol · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains A, B
- PGE · Triethylene glycol · additive · 6 copies · chains A, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
- 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.76 | 0.89 | 35 | XX8, PEG |
| 2 | 195 | 0.74 | 0.90 | 30 | XX8, PEG |
| 3 | 469 | 0.70 | 0.79 | 44 | PGE, 1PE |
| 4 | 94 | 0.46 | 0.79 | 17 | BNG |
Interfaces
1 interface between chains.
- A–B · 584 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4N4D · Structure of ThiT with AV-38 bound · the same entry in another collection · chain B against B, 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 D8KFM5
- Elsewhere: RCSB PDB 4N4D · PDBe 4N4D · UniProt D8KFM5
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