MolNFT v1 · #189548 · protein
Crystal structure of GH3.6 in complex with an inhibitor
7VKA · Indole-3-acetic acid-amido synthetase GH3.6: “Crystal structure of GH3.6 in complex with an inhibitor”. X-ray diffraction, 2 ligands (AMP, 7IS), 7 pockets (best druggability 0.87). MolNFT v1 #189548 on GenesisL1: 3D structure…
- PDB
- 7VKA
- Type
- protein
- Length
- 1,184 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Indole-3-acetic acid-amido synthetase GH3.6
- EC
- 6.3.2.-
- UniProt
- Q9LSQ4
- Ligands
- AMP, 7IS
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Indole-3-acetic acid-amido synthetase GH3.6 (EC 6.3.2.-) | protein | 595 | 42% helix, 22% strand | Q9LSQ4 |
| B | Indole-3-acetic acid-amido synthetase GH3.6 (EC 6.3.2.-) | protein | 589 | 41% helix, 21% strand | Q9LSQ4 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- 7IS · N-[4-[(6-chloranylpyridazin-3-yl)amino]phenyl]-3-(trifluoromethyl)benzamide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.87 | 0.88 | 110 | AMP, 7IS |
| 2 | 1076 | 0.87 | 0.88 | 107 | AMP, 7IS |
| 3 | 470 | 0.63 | 0.77 | 53 | empty |
| 4 | 194 | 0.56 | 0.80 | 24 | empty |
| 5 | 89 | 0.39 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 153 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7VKA · Crystal Structure of GH3.6 in complex with an inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q9LSQ4 · AlphaFold monomer V2.0 prediction for indole-3-acetic acid-amido synthetase GH3.6 (Q9LSQ4) · a predicted model of the same protein · chain B 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 Q9LSQ4
- Elsewhere: RCSB PDB 7VKA · PDBe 7VKA · UniProt Q9LSQ4
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