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Crystal structure of human dipeptidyl peptidase I (cathepsin C) in complex with the inhibitor gly-phe-CHN2
Analyse Crystal structure of human dipeptidyl peptidase I (cathepsin C) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DJF
- Type
- protein
- Length
- 347 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
- 1ZB, NAG, CL
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl-peptidase 1 (EC 3.4.14.1) | protein | 118 | 6% helix, 62% 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
- 1ZB · N-[(1S)-1-benzyl-3-diazen-1-iumylidene-2-oxopropyl]glycinamide · ligand · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, B
- CL · Chloride ion · ion · chains B, C
- ACY · Acetic acid · additive · chains A
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 | 65 | 0.48 | 0.84 | 25 | CL, 1ZB |
| 2 | 87 | 0.40 | 0.77 | 18 | ACY |
| 3 | 56 | 0.35 | 0.79 | 17 | empty |
| 4 | 50 | 0.27 | 0.74 | 12 | empty |
Interfaces
3 interfaces between chains.
- B–C · 3019 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 974 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 350 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 4 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 2DJF · Crystal Structure of human dipeptidyl peptidase I (Cathepsin C) in complex with the… · 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 2DJF · PDBe 2DJF · UniProt P53634
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