Research workbench
X-ray crystal structure of aif-2B alpha subunit-related translation initiation factor [thermotoga maritima]
Analyse X-ray crystal structure of aif-2B alpha subunit-related translation initiation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T9K
- Type
- protein
- Length
- 1,364 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable methylthioribose-1-phosphate isomerase
- EC
- 5.3.1.23
- UniProt
- Q9X013
- Ligands
- SO4, CL
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable methylthioribose-1-phosphate isomerase (EC 5.3.1.23) | protein | 340 | 43% helix, 19% strand | Q9X013 |
| C, D | Probable methylthioribose-1-phosphate isomerase (EC 5.3.1.23) | protein | 342 | 39% helix, 18% strand | Q9X013 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.76 | 0.99 | 21 | empty |
| 2 | 61 | 0.73 | 0.99 | 31 | SO4 |
| 3 | 66 | 0.73 | 0.98 | 30 | SO4 |
| 4 | 61 | 0.72 | 0.99 | 28 | SO4 |
| 5 | 59 | 0.72 | 0.98 | 25 | SO4 |
Interfaces
2 interfaces between chains.
- A–B · 2463 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2457 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 1T9K · X-ray crystal structure of aIF-2B alpha subunit-related translation initiation factor… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9X013 · AlphaFold monomer V2.0 prediction for methylthioribose-1-phosphate isomerase (Q9X013) · 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 Q9X013
- Elsewhere: RCSB PDB 1T9K · PDBe 1T9K · UniProt Q9X013
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