5QC2

Crystal structure of human Cathepsin-S with bound ligand

PDB DOI: https://doi.org/10.2210/pdb5QC2/pdb
Deposition Group: G_1002040 ExploreG_1002040

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2017-08-04 Released: 2017-12-20
Deposition Author(s): Bembenek, S.D., Ameriks, M.K., Mirzadegan, T., Yang, H., Shao, C., Burley, S.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.210
R-Value Work: 0.142
R-Value Observed: 0.145

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of human Cathepsin-S with bound ligand

Bembenek, S.D., Ameriks, M.K., Mirzadegan, T., Yang, H., Shao, C., Burley, S.K.

To be published.

Macromolecule Content

Total Structure Weight: 50.45 kDa
Atom Count: 3,867
Modelled Residue Count: 438
Deposited Residue Count: 446
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin S	A, B	223	Homo sapiens	Mutation(s): 1 Gene Names: CTSS 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
BQP Query on BQP 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]	C [auth A], D [auth B]	2-[1-(cyclohexylmethyl)piperidin-4-yl]-1-{3-[3-{[2-(4-fluoropiperidin-1-yl)ethyl]sulfanyl}-4-(trifluoromethyl)phenyl]-1-(3-hydroxypropyl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl}ethan-1-one C₃₇ H₅₃ F₄ N₅ O₂ S HHMNMVKIYRQSRB-UHFFFAOYSA-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: 2.26 Å
R-Value Free: 0.210
R-Value Work: 0.142
R-Value Observed: 0.145
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.974	α = 70.6
b = 53.635	β = 72.11
c = 58.487	γ = 73.58

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 1.1: 2018-02-21
Changes: Structure summary
Version 2.0: 2018-06-06
Changes: Atomic model, Data collection, Refinement description
Version 2.1: 2021-02-10
Changes: Database references, Structure summary
Version 2.2: 2021-11-17
Changes: Database references, Structure summary

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Help and Resources

5QC2

Crystal structure of human Cathepsin-S with bound ligand

Crystal structure of human Cathepsin-S with bound ligand

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)