4OEL

Crystal structure of Cathepsin C in complex with dipeptide substrates

• PDB DOI: https://doi.org/10.2210/pdb4OEL/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2014-01-13 Released: 2015-03-25 
• Deposition Author(s): Zhao, B., Smallwood, A., Concha, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.198 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.74 kDa 
• Atom Count: 3,134 
• Modelled Residue Count: 350 
• Deposited Residue Count: 440 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 1 Heavy chain	A	370	Homo sapiens	Mutation(s): 1  Gene Names: CPPI, 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 1 Light chain	B	70	Homo sapiens	Mutation(s): 0  Gene Names: CTSC, CPPI 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
TYR	D [auth A]	TYROSINE C9 H11 N O3 OUYCCCASQSFEME-QMMMGPOBSA-N
SER	C [auth A]	SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.198 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.52	α = 90
b = 89.258	β = 90
c = 115.342	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Zhao, B., Smallwood, A., Concha, N.

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary