Research workbench
Structure of organellar oligopeptidase (E572Q) in complex with an endogenous substrate
Analyse Structure of organellar oligopeptidase (E572Q) in complex with an endogenous… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KA7
- Type
- protein
- Length
- 699 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligopeptidase a; Short endogenous peptide substrate
- UniProt
- Q9LSL3
- Ligands
- ZN, NA, CL
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oligopeptidase a | protein | 695 | 60% helix, 7% strand | Q9LSL3 |
| C | Short endogenous peptide substrate | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A, C
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 3 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.84 | 0.90 | 65 | empty |
| 2 | 396 | 0.76 | 0.86 | 42 | empty |
| 3 | 255 | 0.76 | 0.90 | 45 | empty |
| 4 | 245 | 0.56 | 0.78 | 33 | GOL |
| 5 | 53 | 0.54 | 0.89 | 9 | empty |
Interfaces
1 interface between chains.
- A–C · 338 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4KA7 · Structure of Organellar OligoPeptidase (E572Q) in complex with an endogenous substrate · 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 4KA7 · PDBe 4KA7 · UniProt Q9LSL3
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