Research workbench
Structure of a eukaryotic thiaminase-I bound to the thiamin analogue 3-deazathiamin
Analyse Structure of a eukaryotic thiaminase-I bound to the thiamin analogue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HCY
- Type
- protein
- Length
- 2,112 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiaminase-I
- EC
- 2.5.1.2
- UniProt
- D2V4Z5
- Ligands
- 0YN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Thiaminase-I (EC 2.5.1.2) | protein | 352 | 44% helix, 20% strand | D2V4Z5 |
Ligands and binding sites
- 0YN · 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophen-2-yl}ethanol · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.84 | 0.90 | 66 | 0YN |
| 2 | 452 | 0.82 | 0.90 | 66 | 0YN |
| 3 | 451 | 0.82 | 0.89 | 61 | 0YN |
| 4 | 401 | 0.81 | 0.89 | 59 | 0YN |
| 5 | 396 | 0.81 | 0.89 | 57 | 0YN |
Interfaces
5 interfaces between chains.
- D–E · 1092 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1031 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1026 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 978 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 956 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4HCY · Structure of a eukaryotic thiaminase-I bound to the thiamin analogue 3-deazathiamin · 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 D2V4Z5
- Elsewhere: RCSB PDB 4HCY · PDBe 4HCY · UniProt D2V4Z5
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