2G6D | pdb_00002g6d

Human cathepsin S mutant with vinyl sulfone inhibitor CRA-14009

PDB DOI: https://doi.org/10.2210/pdb2G6D/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2006-02-24 Released: 2006-04-04
Deposition Author(s): Somoza, J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.227 (Depositor), 0.220 (DCC)
R-Value Work:
0.192 (Depositor), 0.190 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Human cathepsin S mutant with vinyl sulfone inhibitor CRA-14009

Somoza, J.R.

To be published.

Macromolecule Content

Total Structure Weight: 24.72 kDa
Atom Count: 1,762
Modeled Residue Count: 217
Deposited Residue Count: 217
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cathepsin S	A	217	Homo sapiens	Mutation(s): 2 EC: 3.4.22.27
UniProt & NIH Common Fund Data Resources
Find proteins for P25774 (Homo sapiens) Explore P25774 Go to UniProtKB: P25774
PHAROS: P25774 GTEx: ENSG00000163131
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25774
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MQQ Query on MQQ Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-[(1S)-1-[({(1S)-3-PHENYL-1-[2-(PHENYLSULFONYL)ETHYL]PROPYL}AMINO)CARBONYL]-3-(PHENYLSULFONYL)PROPYL]MORPHOLINE-4-CARBOXAMIDE C₃₂ H₃₉ N₃ O₇ S₂ UBNUVKZLXUKEGC-FIBWVYCGSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.227 (Depositor), 0.220 (DCC)
R-Value Work: 0.192 (Depositor), 0.190 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.47	α = 90
b = 85.89	β = 90
c = 116.26	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-04-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-04-04
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2021-10-20
Changes: Database references, Derived calculations
Version 1.5: 2024-11-13
Changes: Data collection, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.