Research workbench
Crystal structure of a putative myo-inositol dehydrogenase from sinorhizobium meliloti 1021 (target psi-012312)
Analyse Crystal structure of a putative myo-inositol dehydrogenase from sinorhizobium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HKT
- Type
- protein
- Length
- 1,317 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol 2-dehydrogenase
- EC
- 1.1.1.18
- UniProt
- O68965
- Ligands
- NA
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Inositol 2-dehydrogenase (EC 1.1.1.18) | protein | 329 | 41% helix, 25% strand | O68965 |
| B | Inositol 2-dehydrogenase (EC 1.1.1.18) | protein | 330 | 42% helix, 26% strand | O68965 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.87 | 0.89 | 101 | EDO, GOL |
| 2 | 340 | 0.69 | 0.82 | 39 | empty |
| 3 | 439 | 0.69 | 0.80 | 38 | empty |
| 4 | 495 | 0.69 | 0.79 | 42 | empty |
| 5 | 315 | 0.68 | 0.82 | 34 | EDO |
Interfaces
6 interfaces between chains.
- A–B · 1605 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1572 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 937 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 925 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 623 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 modified (engineered).
Compared structures
- 4HKT · Crystal structure of a putative myo-inositol dehydrogenase from Sinorhizobium meliloti… · the same entry in another collection · chain A against A, TM-score 1.00
- O68965 · AlphaFold monomer V2.0 prediction for inositol 2-dehydrogenase (O68965) · 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 O68965
- Elsewhere: RCSB PDB 4HKT · PDBe 4HKT · UniProt O68965
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