Research workbench
Crystal structure of a putative dihydrofolate reductase (BSU40760, yyap) from bacillus subtilis at 2.30 a resolution
Analyse Crystal structure of a putative dihydrofolate reductase (BSU40760, yyap) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GD9
- Type
- protein
- Length
- 348 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein yyap
- UniProt
- P37508
- Ligands
- PO4, CL
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein yyap | protein | 177 | 24% helix, 33% strand | P37508 |
| B | Hypothetical protein yyap | protein | 171 | 27% helix, 32% strand | P37508 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 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 | 406 | 0.73 | 0.83 | 40 | PO4, EDO |
| 2 | 491 | 0.72 | 0.81 | 49 | CL, PO4, EDO |
| 3 | 181 | 0.61 | 0.82 | 31 | EDO |
Interfaces
1 interface between chains.
- A–B · 1186 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2GD9 · Crystal structure of a putative dihydrofolate reductase (bsu40760, yyap) from bacillus… · the same entry in another collection · chain A against A, TM-score 1.00
- P37508 · AlphaFold monomer V2.0 prediction for uncharacterized protein yyap (P37508) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P37508
- Elsewhere: RCSB PDB 2GD9 · PDBe 2GD9 · UniProt P37508
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.