MolNFT v1 · #71569 · protein
Homocitrate synthase LYS4 bound to lysine
3MI3 · Homocitrate synthase, mitochondrial: “Homocitrate synthase LYS4 bound to lysine”. X-ray diffraction, 3 ligands (LYS, ZN, NA), 5 pockets (best druggability 0.75). MolNFT v1 #71569 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3MI3
- Type
- protein
- Length
- 739 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
- LYS, ZN, NA
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homocitrate synthase, mitochondrial (EC 2.3.3.14) | protein | 370 | 48% helix, 14% strand | Q9Y823 |
| B | Homocitrate synthase, mitochondrial (EC 2.3.3.14) | protein | 369 | 48% helix, 14% strand | Q9Y823 |
Ligands and binding sites
- LYS · Lysine · 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
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.75 | 0.95 | 35 | LYS, ZN |
| 2 | 102 | 0.75 | 0.96 | 24 | empty |
| 3 | 120 | 0.70 | 0.92 | 32 | LYS, ZN |
| 4 | 180 | 0.68 | 0.87 | 31 | empty |
| 5 | 218 | 0.68 | 0.85 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 4126 Ų buried · 59 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 3MI3 · PDBe 3MI3 · UniProt Q9Y823
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