MolNFT v1 · #67821 · protein
Homocitrate synthase LYS4
3IVS · Homocitrate synthase, mitochondrial: “Homocitrate synthase LYS4”. X-ray diffraction, 2 ligands (CO, MG), 6 pockets (best druggability 0.77). MolNFT v1 #67821 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3IVS
- Type
- protein
- Length
- 723 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
- CO, MG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homocitrate synthase, mitochondrial (EC 2.3.3.14) | protein | 364 | 44% helix, 15% strand | Q9Y823 |
| B | Homocitrate synthase, mitochondrial (EC 2.3.3.14) | protein | 359 | 47% helix, 15% strand | Q9Y823 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.77 | 0.97 | 23 | empty |
| 2 | 62 | 0.72 | 0.98 | 20 | CO, MG |
| 3 | 56 | 0.71 | 0.99 | 20 | MG |
| 4 | 158 | 0.65 | 0.86 | 27 | empty |
| 5 | 151 | 0.61 | 0.84 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 4008 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
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 3IVS · PDBe 3IVS · UniProt Q9Y823
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