2FUD | pdb_00002fud

Human Cathepsin S with Inhibitor CRA-27566

PDB DOI: https://doi.org/10.2210/pdb2FUD/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2006-01-26 Released: 2006-08-01
Deposition Author(s): Somoza, J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.217 (Depositor), 0.217 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.193 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Human Cathepsin S with Inhibitor CRA-27566

Somoza, J.R.

To be published.

Macromolecule Content

Total Structure Weight: 50.87 kDa
Atom Count: 3,717
Modeled Residue Count: 435
Deposited Residue Count: 450
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cathepsin S	A, B	225	Homo sapiens	Mutation(s): 0 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
CRL Query on CRL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	N-{(1R)-2-[(4-CYANO-1,1-DIOXIDOTETRAHYDRO-2H-THIOPYRAN-4-YL)AMINO]-2-OXO-1-[(TRIMETHYLSILYL)METHYL]ETHYL}MORPHOLINE-4-CARBOXAMIDE C₁₇ H₃₀ N₄ O₅ S Si VASVHRZIUGJLOH-AWEZNQCLSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.217 (Depositor), 0.217 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.42	α = 90
b = 85.42	β = 90
c = 151.99	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
EPMR	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-08-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-08-01
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: 2024-11-06
Changes: Data collection, Database references, Derived calculations, 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.