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Crystal structure of 5-methylthioribose 1-phosphate isomerase from pyrococcus horikoshii OT3 - form II
Analyse Crystal structure of 5-methylthioribose 1-phosphate isomerase from pyrococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A35
- Type
- protein
- Length
- 1,424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative methylthioribose-1-phosphate isomerase
- EC
- 5.3.1.23
- UniProt
- O58433
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative methylthioribose-1-phosphate isomerase (EC 5.3.1.23) | protein | 356 | 46% helix, 18% strand | O58433 |
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.77 | 0.81 | 79 | empty |
| 2 | 735 | 0.76 | 0.81 | 77 | empty |
| 3 | 772 | 0.75 | 0.80 | 75 | empty |
| 4 | 702 | 0.75 | 0.81 | 61 | empty |
| 5 | 438 | 0.75 | 0.84 | 47 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2197 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2186 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 672 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 655 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6A35 · Crystal structure of 5-methylthioribose 1-phosphate isomerase from Pyrococcus horikoshii… · the same entry in another collection · chain A against A, TM-score 1.00
- O58433 · AlphaFold monomer V2.0 prediction for putative methylthioribose-1-phosphate isomerase… · a predicted model of the same protein · chain A against A, TM-score 0.93
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 O58433
- Elsewhere: RCSB PDB 6A35 · PDBe 6A35 · UniProt O58433
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