MolNFT v1 · #58079 · protein
Crystal structure of homoisocitrate dehydrogenase in complex with a designed inhibitor
3ASJ: “Crystal structure of homoisocitrate dehydrogenase in complex with a designed inhibitor”. X-ray diffraction, 2 ligands (XYM, XYN), 11 pockets (best druggability 0.74). MolNFT v1 #58079 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3ASJ
- Type
- protein
- Length
- 1,332 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoisocitrate dehydrogenase
- UniProt
- Q8RQU4
- Ligands
- XYM, XYN
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Homoisocitrate dehydrogenase | protein | 333 | 43% helix, 22% strand | Q8RQU4 |
Ligands and binding sites
- XYM · (2Z)-3-[(carboxymethyl)sulfanyl]-2-hydroxyprop-2-enoic acid · ligand · 2 copies · chains A, B, C, D
- XYN · 3-[(carboxymethyl)sulfanyl]-2-oxopropanoic acid · ligand · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 19 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.74 | 0.77 | 107 | MPD |
| 2 | 724 | 0.73 | 0.79 | 62 | XYM, MPD |
| 3 | 788 | 0.73 | 0.78 | 83 | XYN, MPD |
| 4 | 592 | 0.72 | 0.80 | 46 | XYM |
| 5 | 408 | 0.69 | 0.80 | 37 | MPD |
Interfaces
6 interfaces between chains.
- C–D · 2036 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2026 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 414 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 412 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 219 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3ASJ · Crystal structure of homoisocitrate dehydrogenase in complex with a designed inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8RQU4
- Elsewhere: RCSB PDB 3ASJ · PDBe 3ASJ · UniProt Q8RQU4
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