Research workbench
Crystal structure of cathepsin C in complex with dipeptide substrates
Analyse Crystal structure of cathepsin C in complex with dipeptide substrates in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OEL
- Type
- protein
- Length
- 352 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 1 heavy chain; Dipeptidyl peptidase 1 light chain
- EC
- 3.4.14.1
- UniProt
- P53634
- Ligands
- NAG, CL
- Pockets
- 4 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 1 heavy chain (EC 3.4.14.1) | protein | 283 | 22% helix, 34% strand | P53634 |
| B | Dipeptidyl peptidase 1 light chain (EC 3.4.14.1) | protein | 69 | 4% helix, 41% strand | P53634 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.37 | 0.77 | 15 | empty |
| 2 | 67 | 0.34 | 0.77 | 18 | empty |
| 3 | 66 | 0.34 | 0.76 | 17 | empty |
| 4 | 53 | 0.28 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 3286 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4OEL · Crystal structure of Cathepsin C in complex with dipeptide substrates · the same entry in another collection · chain A against A, TM-score 1.00
- P53634 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 1 (P53634) · 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 P53634
- Elsewhere: RCSB PDB 4OEL · PDBe 4OEL · UniProt P53634
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