Research workbench
Structure of organellar oligopeptidase
Analyse Structure of organellar oligopeptidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KA8
- Type
- protein
- Length
- 695 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligopeptidase a
- UniProt
- Q9LSL3
- Ligands
- ZN, NA, CL
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 60% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oligopeptidase a | protein | 695 | 60% helix, 7% strand | Q9LSL3 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 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
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.77 | 0.90 | 29 | empty |
| 2 | 219 | 0.75 | 0.89 | 34 | GOL |
| 3 | 182 | 0.71 | 0.89 | 37 | empty |
| 4 | 172 | 0.67 | 0.86 | 25 | empty |
| 5 | 147 | 0.60 | 0.84 | 25 | empty |
Compared structures
- 4KA8 · Structure of Organellar OligoPeptidase · 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 Q9LSL3
- Elsewhere: RCSB PDB 4KA8 · PDBe 4KA8 · UniProt Q9LSL3
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