Research workbench
Crystal structure of homoisocitrate dehydrogenase from schizosaccharomyces pombe bound to glycyl-glycyl-glycine
Analyse Crystal structure of homoisocitrate dehydrogenase from schizosaccharomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TY3
- Type
- protein
- Length
- 710 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
- Ligands
- GGG
- Pockets
- 9 · best druggability 0.72
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 | 358 | 45% helix, 20% strand | O14104 |
| B | Probable homoisocitrate dehydrogenase (EC 1.1.1.87) | protein | 352 | 44% helix, 20% strand | O14104 |
Ligands and binding sites
- GGG · glycylglycylglycine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.72 | 0.82 | 55 | GOL |
| 2 | 705 | 0.71 | 0.78 | 57 | GGG |
| 3 | 728 | 0.71 | 0.78 | 54 | GGG |
| 4 | 337 | 0.70 | 0.83 | 33 | empty |
| 5 | 75 | 0.38 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2276 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 3TY3 · Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe bound to… · 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 3TY3 · PDBe 3TY3 · UniProt O14104
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