2DJG
Re-determination of the native structure of human dipeptidyl peptidase I (cathepsin C)
- PDB DOI: https://doi.org/10.2210/pdb2DJG/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Trichoplusia ni
- Mutation(s): No 
- Deposited: 2006-04-02 Released: 2006-11-14 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 Å
- R-Value Free: 0.221 
- R-Value Work: 0.174 
- R-Value Observed: 0.176 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Dipeptidyl-peptidase 1 | 119 | Homo sapiens | Mutation(s): 0  Gene Names: CTSC EC: 3.4.14.1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P53634 (Homo sapiens) Explore P53634  Go to UniProtKB:  P53634 | |||||
PHAROS:  P53634 GTEx:  ENSG00000109861  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P53634 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Dipeptidyl-peptidase 1 | 164 | Homo sapiens | Mutation(s): 0  Gene Names: CTSC EC: 3.4.14.1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P53634 (Homo sapiens) Explore P53634  Go to UniProtKB:  P53634 | |||||
PHAROS:  P53634 GTEx:  ENSG00000109861  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P53634 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Dipeptidyl-peptidase 1 | 69 | Homo sapiens | Mutation(s): 0  Gene Names: CTSC EC: 3.4.14.1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P53634 (Homo sapiens) Explore P53634  Go to UniProtKB:  P53634 | |||||
PHAROS:  P53634 GTEx:  ENSG00000109861  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P53634 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G34771DU GlyCosmos:  G34771DU GlyGen:  G34771DU |
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | E [auth A], G [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
SO4 Query on SO4 | F [auth A], I [auth C] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
CL Query on CL | H [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 Å
- R-Value Free: 0.221 
- R-Value Work: 0.174 
- R-Value Observed: 0.176 
- Space Group: I 2 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 87.479 | α = 90 |
b = 88.68 | β = 90 |
c = 114.35 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
Entry History 
Deposition Data
- Released Date: 2006-11-14  Deposition Author(s): Molgaard, A., Arnau, J., Lauritzen, C., Larsen, S., Petersen, G., Pedersen, J.
Revision History (Full details and data files)
- Version 1.0: 2006-11-14
Type: Initial release - Version 1.1: 2007-12-26
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-25
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary