Research workbench
Structure of trifunctional THI20 from yeast
Analyse Structure of trifunctional THI20 from yeast in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RM5
- Type
- protein
- Length
- 1,040 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HYDROXYMETHYLPYRIMIDINE/PHOSPHOMETHYLPYRIMIDINE kinase THI20
- EC
- 2.7.1.49, 2.7.4.7
- UniProt
- Q08224
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HYDROXYMETHYLPYRIMIDINE/PHOSPHOMETHYLPYRIMIDINE kinase THI20 (EC 2.7.1.49, 2.7.4.7) | protein | 521 | 54% helix, 13% strand | Q08224 |
| B | HYDROXYMETHYLPYRIMIDINE/PHOSPHOMETHYLPYRIMIDINE kinase THI20 (EC 2.7.1.49, 2.7.4.7) | protein | 519 | 55% helix, 11% strand | Q08224 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.78 | 0.80 | 100 | SO4 |
| 2 | 244 | 0.73 | 0.87 | 33 | empty |
| 3 | 627 | 0.72 | 0.79 | 45 | empty |
| 4 | 477 | 0.66 | 0.78 | 56 | empty |
| 5 | 380 | 0.64 | 0.78 | 43 | SO4 |
Interfaces
1 interface between chains.
- A–B · 6952 Ų buried · 102 hydrogen bonds · protein-protein
Compared structures
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 Q08224
- Elsewhere: RCSB PDB 3RM5 · PDBe 3RM5 · UniProt Q08224
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