Research workbench
Crystal structure of homoisocitrate dehydrogenase from schizosaccharomyces pombe
Analyse Crystal structure of homoisocitrate dehydrogenase from schizosaccharomyces pombe in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TY4
- Type
- protein
- Length
- 713 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable homoisocitrate dehydrogenase
- EC
- 1.1.1.87
- UniProt
- O14104
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable homoisocitrate dehydrogenase (EC 1.1.1.87) | protein | 356 | 45% helix, 20% strand | O14104 |
| B | Probable homoisocitrate dehydrogenase (EC 1.1.1.87) | protein | 357 | 45% helix, 21% strand | O14104 |
Ligands and binding sites
- GOL · Glycerol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.73 | 0.81 | 60 | GOL |
| 2 | 759 | 0.71 | 0.77 | 65 | GOL |
| 3 | 396 | 0.71 | 0.82 | 46 | empty |
| 4 | 670 | 0.68 | 0.77 | 50 | GOL |
| 5 | 76 | 0.34 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2309 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 3TY4 · Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe · the same entry in another collection · chain A against A, TM-score 1.00
- O14104 · AlphaFold monomer V2.0 prediction for homoisocitrate dehydrogenase (O14104) · 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 O14104
- Elsewhere: RCSB PDB 3TY4 · PDBe 3TY4 · UniProt O14104
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