Research workbench
Crystal structure of 5-methylthioribose 1-phosphate isomerase from bacillus subtilis complexed with sulfate ion
Analyse Crystal structure of 5-methylthioribose 1-phosphate isomerase from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YRF
- Type
- protein
- Length
- 681 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylthioribose-1-phosphate isomerase
- EC
- 5.3.1.23
- UniProt
- O31662
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylthioribose-1-phosphate isomerase (EC 5.3.1.23) | protein | 340 | 42% helix, 17% strand | O31662 |
| B | Methylthioribose-1-phosphate isomerase (EC 5.3.1.23) | protein | 341 | 42% helix, 18% strand | O31662 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.78 | 0.99 | 24 | empty |
| 2 | 64 | 0.71 | 0.97 | 26 | SO4 |
| 3 | 185 | 0.49 | 0.77 | 26 | empty |
| 4 | 155 | 0.48 | 0.78 | 16 | empty |
| 5 | 56 | 0.39 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2134 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2YRF · Crystal structure of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis… · the same entry in another collection · chain A against A, TM-score 1.00
- O31662 · AlphaFold monomer V2.0 prediction for methylthioribose-1-phosphate isomerase (O31662) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O31662
- Elsewhere: RCSB PDB 2YRF · PDBe 2YRF · UniProt O31662
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