7QNS

Peptide VYEKKP in complex with human cathepsin V C25S mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Peptide VYEKKP in complex with human cathepsin V C25S 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin L2A [auth AA],
B [auth BA]
222Homo sapiensMutation(s): 3 
Gene Names: CTSVCATL2CTSL2CTSUUNQ268/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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60911
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VAL-TYR-GLU-LYS-LYS-PROC [auth PC],
D [auth PB],
E [auth PA]
6synthetic constructMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
I [auth AA]
M [auth BA]
N [auth BA]
P [auth BA]
Q [auth BA]
I [auth AA],
M [auth BA],
N [auth BA],
P [auth BA],
Q [auth BA],
R [auth BA]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
TFA
Query on TFA

Download Ideal Coordinates CCD File 
H [auth AA],
J [auth AA]
trifluoroacetic acid
C2 H F3 O2
DTQVDTLACAAQTR-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth AA],
O [auth BA]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth AA],
K [auth AA],
L [auth BA]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.97α = 90
b = 93.97β = 90
c = 124.06γ = 90
Software Package:
Software NamePurpose
MAINrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Slovenian Research AgencySloveniaP1-0048

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-18
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-09
    Changes: Structure summary