9GJ2 | pdb_00009gj2

Crystal structure of human cathepsin S produced in insect cells in complex with ketoamide 13b

PDB DOI: https://doi.org/10.2210/pdb9GJ2/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2024-08-20 Released: 2024-09-04
Deposition Author(s): Falke, S., Karnicar, K., Usenik, A., Lindic, N., Sekirnik, A., Reinke, P.Y.A., Guenther, S., Turk, D., Meents, A.
Funding Organization(s): Helmholtz Association, German Federal Ministry for Education and Research, Slovenian Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free:
0.162 (Depositor), 0.161 (DCC)
R-Value Work:
0.151 (Depositor), 0.152 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of human cathepsin S produced in insect cells in complex with ketoamide 13b

Falke, S., Karnicar, K., Usenik, A., Lindic, N., Sekirnik, A., Reinke, P.Y.A., Guenther, S., Turk, D., Meents, A.

To be published.

Macromolecule Content

Total Structure Weight: 55.31 kDa
Atom Count: 4,041
Modeled Residue Count: 440
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin S	A, B	242	Homo sapiens	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25774
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KH0 (Subject of Investigation/LOI) Query on KH0 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{S})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate C₃₁ H₄₁ N₅ O₇ FRACPXUHUTXLCX-LFBFJMOVSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B]	D [auth A], E [auth A], I [auth B], K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free: 0.162 (Depositor), 0.161 (DCC)
R-Value Work: 0.151 (Depositor), 0.152 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.102	α = 90
b = 86.102	β = 90
c = 152.045	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Helmholtz Association	Germany	FISCOV
Helmholtz Association	Germany	SFragX
German Federal Ministry for Education and Research	Germany	031B0405
Slovenian Research Agency	Slovenia	P1-0048
Slovenian Research Agency	Slovenia	IO-0048