MolNFT v1 · #98088 · protein
Clostridium botulinum thiaminase I in complex with thiamin
4KYS · Thiamine pyridinylase I: “Clostridium botulinum thiaminase I in complex with thiamin”. X-ray diffraction, 2 ligands (VIB, MG), 3 pockets (best druggability 0.78). MolNFT v1 #98088 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4KYS
- Type
- protein
- Length
- 731 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiamine pyridinylase I
- EC
- 2.5.1.2
- UniProt
- A7FS27
- Ligands
- VIB, MG
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamine pyridinylase I (EC 2.5.1.2) | protein | 366 | 43% helix, 20% strand | A7FS27 |
| B | Thiamine pyridinylase I (EC 2.5.1.2) | protein | 365 | 44% helix, 19% strand | A7FS27 |
Ligands and binding sites
- VIB · 3-(4-amino-2-methyl-pyrimidin-5-ylmethyl)-5-(2-hydroxy-ethyl)-4-methyl-thiazol-3-ium · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CIT · Citric acid · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.78 | 0.87 | 53 | VIB, CIT, MG |
| 2 | 433 | 0.77 | 0.85 | 55 | VIB, CIT |
| 3 | 1044 | 0.72 | 0.76 | 100 | empty |
Interfaces
1 interface between chains.
- A–B · 255 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4KYS · Clostridium botulinum thiaminase I in complex with thiamin · 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 A7FS27
- Elsewhere: RCSB PDB 4KYS · PDBe 4KYS · UniProt A7FS27
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.