Research workbench
Crystal structure of semet derivative of hmp synthase THI5 from S. cerevisiae
Analyse Crystal structure of semet derivative of hmp synthase THI5 from S. cerevisiae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H65
- Type
- protein
- Length
- 581 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrimidine precursor biosynthesis enzyme THI5
- UniProt
- P43534
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrimidine precursor biosynthesis enzyme THI5 | protein | 315 | 44% helix, 17% strand | P43534 |
| B | Pyrimidine precursor biosynthesis enzyme THI5 | protein | 266 | 44% helix, 15% strand | P43534 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.81 | 0.82 | 102 | empty |
| 2 | 638 | 0.75 | 0.81 | 71 | empty |
| 3 | 386 | 0.65 | 0.79 | 37 | empty |
| 4 | 201 | 0.47 | 0.75 | 34 | empty |
| 5 | 67 | 0.38 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1412 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 4H65 · Crystal structure of SeMet derivative of HMP synthase Thi5 from S. cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
- P43534 · AlphaFold monomer V2.0 prediction for 4-amino-5-hydroxymethyl-2-methylpyrimidine… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P43534
- Elsewhere: RCSB PDB 4H65 · PDBe 4H65 · UniProt P43534
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