MolNFT v1 · #163965 · protein
Amidohydrolase, ahs with 3-hba
6SJ3: “Amidohydrolase, ahs with 3-hba”. X-ray diffraction, 3 ligands (3HB, ZN, MG), 8 pockets (best druggability 0.79). MolNFT v1 #163965 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6SJ3
- Type
- protein
- Length
- 997 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amidohydrolase
- UniProt
- A0A022MQ12
- Ligands
- 3HB, ZN, MG
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amidohydrolase | protein | 494 | 41% helix, 19% strand | A0A022MQ12 |
| B | Amidohydrolase | protein | 503 | 41% helix, 19% strand | A0A022MQ12 |
Ligands and binding sites
- 3HB · 3-hydroxybenzoic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- GOL · Glycerol · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.79 | 0.86 | 68 | 3HB, PEG |
| 2 | 455 | 0.79 | 0.87 | 72 | 3HB, GOL |
| 3 | 762 | 0.76 | 0.81 | 83 | empty |
| 4 | 240 | 0.65 | 0.83 | 25 | empty |
| 5 | 99 | 0.45 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3649 Ų buried · 59 hydrogen bonds · protein-protein
Compared structures
- 6SJ3 · Amidohydrolase, AHS with 3-HBA · 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 A0A022MQ12
- Elsewhere: RCSB PDB 6SJ3 · PDBe 6SJ3 · UniProt A0A022MQ12
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