7QO2

Peptide GAKSAA in complex with human cathepsin V C25A mutant

• PDB DOI: https://doi.org/10.2210/pdb7QO2/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Komagataella phaffii GS115
• Mutation(s): Yes 


• Deposited: 2021-12-23 Released: 2023-01-18 
• Deposition Author(s): Loboda, J., Sosnowski, P., Tusar, L., Vidmar, R., Vizovisek, M., Horvat, J., Kosec, G., Impens, F., Demol, H., Turk, B., Gevaert, K., Turk, D.
• Funding Organization(s): Slovenian Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.202 
• R-Value Work: 0.176 
• R-Value Observed: 0.176 

Literature

Peptide GAKSAA in complex with human cathepsin V C25A mutant

Loboda, J., Sosnowski, P., Tusar, L., Vidmar, R., Vizovisek, M., Horvat, J., Kosec, G., Impens, F., Demol, H., Turk, B., Gevaert, K., Turk, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 50.77 kDa 
• Atom Count: 3,997 
• Modelled Residue Count: 454 
• Deposited Residue Count: 459 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin L2	A [auth AA], B [auth BA]	222	Homo sapiens	Mutation(s): 3  Gene Names: CTSV, CATL2, CTSL2, CTSU, UNQ268/PRO305 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
GAKSAA Peptide	C [auth PAA], D [auth PAB]	6	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
EYS Peptide	E [auth PB]	3	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	F [auth AA], G [auth AA], K [auth AA], L [auth BA], Q [auth BA]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
TFA	N [auth BA]	trifluoroacetic acid C2 H F3 O2 DTQVDTLACAAQTR-UHFFFAOYSA-N
GOL	I [auth AA], O [auth BA], P [auth BA]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	H [auth AA], J [auth AA], M [auth BA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.202 
• R-Value Work: 0.176 
• R-Value Observed: 0.176 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.28	α = 90
b = 94.28	β = 90
c = 126.76	γ = 90

Software Package:

Software Name	Purpose
MAIN	refinement
XDS	data reduction
XDS	data scaling
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Loboda, J., Sosnowski, P., Tusar, L., Vidmar, R., Vizovisek, M., Horvat, J., Kosec, G., Impens, F., Demol, H., Turk, B., Gevaert, K., Turk, D.

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Funding Organization	Location	Grant Number
Slovenian Research Agency	Slovenia	P1-0048

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description