2FYE | pdb_00002fye

Mutant Human Cathepsin S with irreversible inhibitor CRA-14013

PDB DOI: https://doi.org/10.2210/pdb2FYE/pdb

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

Deposited: 2006-02-07 Released: 2006-08-08
Deposition Author(s): Somoza, J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.210 (Depositor), 0.211 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2FYE

Ligand Structure Quality Assessment

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

Literature

Mutant Human Cathepsin S with irreversible inhibitor CRA-14013

Somoza, J.R.

To be published.

Macromolecule Content

Total Structure Weight: 24.68 kDa
Atom Count: 1,763
Modeled Residue Count: 217
Deposited Residue Count: 217
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cathepsin S preproprotein	A	217	Homo sapiens	Mutation(s): 4 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25774
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCQ Query on BCQ 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-[(1R)-1-[({[(5S)-3,5-DIMETHYL-2,5-DIHYDROISOXAZOL-4-YL]METHYL}SULFONYL)METHYL]-2-OXO-2-({(1S)-3-PHENYL-1-[2-(PHENYLSULFONYL)ETHYL]PROPYL}AMINO)ETHYL]MORPHOLINE-4-CARBOXAMIDE C₃₁ H₄₂ N₄ O₈ S₂ KPLOSZKQTFPNFM-MIUCGUHXSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.210 (Depositor), 0.211 (DCC)
R-Value Work: 0.194 (Depositor), 0.194 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.58	α = 90
b = 85.43	β = 90
c = 116.26	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-08-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-08-08
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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.