MolNFT v1 · #82759 · protein
Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/R187S/H266N/D370Y mutant complexd with 6-aminohexanoate
3VWP: “Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/R187S/H266N/D370Y mutant complexd with…”. X-ray diffraction, 3 ligands (ACA, NA, SO4), 3 pockets (best druggability 0.66). MolNFT v1 #82759 on GenesisL1: 3D…
- PDB
- 3VWP
- 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, NA, SO4
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-aminohexanoate-dimer hydrolase (EC 3.5.1.46) | protein | 384 | 34% helix, 15% strand | P07061, Q59710 |
Ligands and binding sites
- ACA · 6-aminohexanoic acid · ligand · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 4 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.66 | 0.80 | 43 | ACA, GOL |
| 2 | 109 | 0.39 | 0.75 | 14 | empty |
| 3 | 86 | 0.32 | 0.74 | 21 | empty |
Compared structures
- 3VWP · Crystal structure of 6-aminohexanoate-dimer hydrolase S112A/G181D/R187S/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 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 P07061
- Every structure of UniProt Q59710
- Elsewhere: RCSB PDB 3VWP · PDBe 3VWP · UniProt P07061 · UniProt Q59710
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