MolNFT v1 · #140120 · protein
Structure of 6-aminohexanoate-oligomer hydrolase from arthrobacter sp. KI72., D36A/D122G/H130Y/E263Q muntant
5Y0M · Endo-type 6-aminohexanoate oligomer hydrolase: “Structure of 6-aminohexanoate-oligomer hydrolase from arthrobacter sp. KI72., D36A/D122G/H130Y/E263Q muntant”. X-ray diffraction, 2 ligands (CL, PO4), 3 pockets (best druggability…
- PDB
- 5Y0M
- Type
- protein
- Length
- 661 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-type 6-aminohexanoate oligomer hydrolase
- UniProt
- Q57326
- Ligands
- CL, PO4
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-type 6-aminohexanoate oligomer hydrolase | protein | 329 | 26% helix, 33% strand | Q57326 |
| B | Endo-type 6-aminohexanoate oligomer hydrolase | protein | 332 | 27% helix, 33% strand | Q57326 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.71 | 0.78 | 94 | GOL, CL |
| 2 | 68 | 0.71 | 0.96 | 28 | GOL |
| 3 | 57 | 0.31 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1327 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5Y0M · Structure of 6-aminohexanoate-oligomer hydrolase from Arthrobacter sp. KI72.… · 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 Q57326
- Elsewhere: RCSB PDB 5Y0M · PDBe 5Y0M · UniProt Q57326
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