2DJF

Crystal Structure of human dipeptidyl peptidase I (Cathepsin C) in complex with the inhibitor Gly-Phe-CHN2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl-peptidase 1119Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53634
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl-peptidase 1164Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53634
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl-peptidase 169Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53634
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1ZB
Query on 1ZB
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J [auth B]N-[(1S)-1-benzyl-3-diazen-1-iumylidene-2-oxopropyl]glycinamide
C12 H14 N4 O2
CBOIZHHBFFTMCQ-JTQLQIEISA-N
NAG
Query on NAG
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D [auth A],
E [auth A],
F [auth A],
H [auth B]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ACY
Query on ACY
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G [auth A]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
I [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87α = 90
b = 89.03β = 90
c = 115.57γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2018-05-23
    Changes: Advisory, Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-10-25
    Changes: Data collection, Database references, Refinement description, Structure summary