Research workbench
Structure of 6-aminohexanoate-dimer hydrolase, A61V/A124V/R187S/F264C/G291R/G338A/D370Y mutant (hyb-S4M94)
Analyse 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
- 2ZM2
- 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, P07062
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.67
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, P07062 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A
- GOL · Glycerol · additive · 4 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 | 417 | 0.67 | 0.79 | 44 | MES, GOL |
| 2 | 108 | 0.38 | 0.75 | 14 | empty |
| 3 | 88 | 0.33 | 0.74 | 22 | empty |
Compared structures
- 2ZM2 · Structure of 6-aminohexanoate-dimer hydrolase, A61V/A124V/R187S/F264C/G291R/G338A/D370Y… · the same entry in another collection · chain A against A, TM-score 1.00
- P07062 · AlphaFold monomer V2.0 prediction for 6-aminohexanoate-dimer hydrolase (P07062) · a predicted model of the same protein · chain A against A, TM-score 0.99
- 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 P07062
- Elsewhere: RCSB PDB 2ZM2 · PDBe 2ZM2 · UniProt P07061 · UniProt P07062
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