MolNFT v1 · #25692 · protein
Crystal structure of yeast YPR118W, a methylthioribose-1-phosphate isomerase related to regulatory EIF2B subunits
1W2W · 5-methylthioribose-1-phosphate isomerase: “Crystal structure of yeast YPR118W, a methylthioribose-1-phosphate isomerase related to regulatory EIF2B…”. X-ray diffraction, 1 ligand (SO4), 16 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 1W2W
- Type
- protein
- Length
- 1,607 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-methylthioribose-1-phosphate isomerase
- EC
- 5.3.1.23
- UniProt
- Q06489
- Ligands
- SO4
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | 5-methylthioribose-1-phosphate isomerase (EC 5.3.1.23) | protein | 211 | 59% helix, 9% strand | Q06489 |
| B, F, J, N | 5-methylthioribose-1-phosphate isomerase (EC 5.3.1.23) | protein | 191 | 26% helix, 31% strand | Q06489 |
| M | 5-methylthioribose-1-phosphate isomerase (EC 5.3.1.23) | protein | 210 | 58% helix, 9% strand | Q06489 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, E, F, I, J, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.72 | 0.98 | 30 | SO4 |
| 2 | 63 | 0.72 | 0.98 | 31 | SO4 |
| 3 | 53 | 0.71 | 0.98 | 25 | SO4 |
| 4 | 56 | 0.70 | 0.98 | 24 | SO4 |
| 5 | 219 | 0.60 | 0.81 | 42 | empty |
Interfaces
12 interfaces between chains.
- A–B · 3246 Ų buried · 50 hydrogen bonds · protein-protein
- E–F · 3217 Ų buried · 48 hydrogen bonds · protein-protein
- I–J · 3212 Ų buried · 48 hydrogen bonds · protein-protein
- M–N · 3200 Ų buried · 48 hydrogen bonds · protein-protein
- F–J · 2704 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 modified (engineered).
Compared structures
- 1W2W · Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to… · the same entry in another collection · chain N against N, TM-score 1.00
- Q06489 · AlphaFold monomer V2.0 prediction for methylthioribose-1-phosphate isomerase (Q06489) · a predicted model of the same protein · chain A 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 Q06489
- Elsewhere: RCSB PDB 1W2W · PDBe 1W2W · UniProt Q06489
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