Research workbench
Homocitrate synthase LYS4 bound to 2-og
Analyse Homocitrate synthase LYS4 bound to 2-og in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IVT
- Type
- protein
- Length
- 798 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homocitrate synthase, mitochondrial
- EC
- 2.3.3.14
- UniProt
- Q9Y823
- Ligands
- AKG, ZN, NA
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homocitrate synthase, mitochondrial (EC 2.3.3.14) | protein | 398 | 45% helix, 17% strand | Q9Y823 |
| B | Homocitrate synthase, mitochondrial (EC 2.3.3.14) | protein | 400 | 45% helix, 17% strand | Q9Y823 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.77 | 0.97 | 24 | empty |
| 2 | 77 | 0.74 | 0.98 | 24 | AKG |
| 3 | 59 | 0.71 | 0.98 | 25 | AKG |
| 4 | 127 | 0.70 | 0.91 | 27 | empty |
| 5 | 131 | 0.68 | 0.89 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 5625 Ų buried · 96 hydrogen bonds · protein-protein
Compared structures
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 Q9Y823
- Elsewhere: RCSB PDB 3IVT · PDBe 3IVT · UniProt Q9Y823
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