Research workbench
Re-determination of the native structure of human dipeptidyl peptidase I (cathepsin C)
Analyse Re-determination of the native structure of human dipeptidyl peptidase I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DJG
- Type
- protein
- Length
- 343 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl-peptidase 1
- EC
- 3.4.14.1
- UniProt
- P53634
- Ligands
- NAG, BMA, SO4, CL
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl-peptidase 1 (EC 3.4.14.1) | protein | 114 | 6% helix, 59% strand | P53634 |
| B | Dipeptidyl-peptidase 1 (EC 3.4.14.1) | protein | 161 | 33% helix, 15% strand | P53634 |
| C | Dipeptidyl-peptidase 1 (EC 3.4.14.1) | protein | 68 | 4% helix, 41% strand | P53634 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C
- CL · Chloride ion · ion · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.47 | 0.83 | 23 | CL |
| 2 | 100 | 0.38 | 0.75 | 20 | SO4 |
| 3 | 62 | 0.33 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 3005 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 974 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 353 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 2DJG · Re-determination of the native structure of human dipeptidyl peptidase I (cathepsin C) · 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 B 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 P53634
- Elsewhere: RCSB PDB 2DJG · PDBe 2DJG · UniProt P53634
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