3KFQ

Unreduced cathepsin V in complex with stefin A

• PDB DOI: https://doi.org/10.2210/pdb3KFQ/pdb

• Classification: Hydrolase/Hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-10-27 Released: 2010-11-03 
• Deposition Author(s): Renko, M., Turk, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.219 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Starting Models: experimental

Literature

Unreduced cathepsin V in complex with stefin A

Renko, M., Turk, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.22 kDa 
• Atom Count: 5,654 
• Modelled Residue Count: 638 
• Deposited Residue Count: 638 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin L2	A, B	221	Homo sapiens	Mutation(s): 2  EC: 3.4.22.43
UniProt & NIH Common Fund Data Resources
Find proteins for O60911 (Homo sapiens) Explore O60911  Go to UniProtKB:  O60911
PHAROS:  O60911 GTEx:  ENSG00000136943

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystatin-A	C, D	98	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01040 (Homo sapiens) Explore P01040  Go to UniProtKB:  P01040
PHAROS:  P01040 GTEx:  ENSG00000121552

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SCH	A, B	L-PEPTIDE LINKING	C4 H9 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.219 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.313	α = 90
b = 107.29	β = 90
c = 115.98	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-03 
Deposition Author(s): Renko, M., Turk, D.

Revision History  

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2023-11-01
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description