1K3B

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

Structural Biology Knowledgebase: 1K3B SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 1K3B

Classification: HYDROLASE

Total Structure Weight: 40120.59

Macromolecule Entities
Molecule Chains Length Organism Details
dipeptydil-peptidase I exclusion domain A 119 Homo sapiens EC#: 3.4.14.1 IUBMB
Gene Name(s): CTSC Gene View CPPI
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
dipeptydil-peptidase I light chain B 164 Homo sapiens EC#: 3.4.14.1 IUBMB
Gene Name(s): CTSC Gene View CPPI
dipeptydil-peptidase I heavy chain C 69 Homo sapiens EC#: 3.4.14.1 IUBMB
Gene Name(s): CTSC Gene View CPPI

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, C SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.190
  • Space Group: I 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 87.15 α = 90.00
b = 88.03 β = 90.00
c = 114.61 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-10-02
  • Released Date: 2002-04-02
  • Deposition author(s): Turk, D., Janjic, V., Stern, I., Podobnik, M., Lamba, D., Dahl, S.W., Lauritzen, C., Pedersen, J., Turk, V., Turk, B.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values