MolNFT v1 · #11994 · protein
Crystal structure of human dipeptidyl peptidase I (cathepsin C): exclusion domain added to an endopeptidase framework creates the machine for activation of granular serine proteases
1K3B · Dipeptydil-peptidase I exclusion domain: “Crystal structure of human dipeptidyl peptidase I (cathepsin C): exclusion domain added to an endopeptidase…”. X-ray diffraction, 3 ligands (NAG, SO4, CL), 5 pockets (best druggability…
- PDB
- 1K3B
- Type
- protein
- Length
- 352 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptydil-peptidase I exclusion domain; Dipeptydil-peptidase I light chain…
- EC
- 3.4.14.1
- UniProt
- P53634
- Ligands
- NAG, SO4, CL
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptydil-peptidase I exclusion domain (EC 3.4.14.1) | protein | 119 | 3% helix, 55% strand | P53634 |
| B | Dipeptydil-peptidase I light chain (EC 3.4.14.1) | protein | 164 | 30% helix, 15% strand | P53634 |
| C | Dipeptydil-peptidase I heavy 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 · chains A, B, C
- SO4 · Sulfate ion · ion · 3 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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.51 | 0.86 | 22 | CL |
| 2 | 87 | 0.39 | 0.77 | 19 | SO4 |
| 3 | 58 | 0.34 | 0.78 | 14 | empty |
| 4 | 55 | 0.34 | 0.78 | 16 | empty |
| 5 | 59 | 0.32 | 0.75 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–C · 3081 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 965 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 356 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1K3B · Crystal Structure of Human Dipeptidyl Peptidase I (Cathepsin C): Exclusion Domain Added… · 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 0.98
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 1K3B · PDBe 1K3B · UniProt P53634
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