Research workbench
Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/R187G/H266N/D370Y mutant complexd with 6-aminohexanoate
Analyse Crystal structure of 6-aminohexanoate-dimer hydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VWR
- Type
- protein
- Length
- 384 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-aminohexanoate-dimer hydrolase
- EC
- 3.5.1.46
- UniProt
- P07061, Q59710
- Ligands
- ACA, SO4
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-aminohexanoate-dimer hydrolase (EC 3.5.1.46) | protein | 384 | 35% helix, 15% strand | P07061, Q59710 |
Ligands and binding sites
- ACA · 6-aminohexanoic acid · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 5 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.67 | 0.81 | 37 | ACA, GOL |
| 2 | 204 | 0.47 | 0.74 | 35 | empty |
Compared structures
- 3VWR · Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/R187G/H266N/D370Y… · the same entry in another collection · chain A against A, TM-score 1.00
- P07061 · AlphaFold monomer V2.0 prediction for 6-aminohexanoate-dimer hydrolase (P07061) · a predicted model of the same protein · 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 P07061
- Every structure of UniProt Q59710
- Elsewhere: RCSB PDB 3VWR · PDBe 3VWR · UniProt P07061 · UniProt Q59710
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