7QKD

Crystal structure of human Cathepsin L in complex with covalently bound MG132

PDB DOI: https://doi.org/10.2210/pdb7QKD/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella phaffii GS115
Mutation(s): Yes

Deposited: 2021-12-17 Released: 2022-12-28
Deposition Author(s): Reinke, P.Y.A., Falke, S., Lieske, J., Ewert, W., Loboda, J., Rahmani Mashhour, A., Hauser, M., Karnicar, K., Usenik, A., Lindic, N., Lach, M., Boehler, H., Beck, T., Cox, R., Chapman, H.N., Hinrichs, W., Turk, D., Guenther, S., 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: 1.50 Å
R-Value Free: 0.198
R-Value Work: 0.180
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Sulfonated Calpeptin is a promising drug candidate against SARS-CoV-2 infections

Reinke, P.Y.A., Falke, S., Lieske, J., Ewert, W., Loboda, J., Rahmani Mashhour, A., Hauser, M., Karnicar, K., Usenik, A., Lindic, N., Lach, M., Boehler, H., Beck, T., Cox, R., Chapman, H.N., Hinrichs, W., Turk, D., Guenther, S., Meents, A.

To be published.

Macromolecule Content

Total Structure Weight: 99.36 kDa
Atom Count: 8,096
Modelled Residue Count: 876
Deposited Residue Count: 880
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 L	A, B, C, D	220	Homo sapiens	Mutation(s): 1 Gene Names: CTSL, CTSL1
UniProt & NIH Common Fund Data Resources
Find proteins for P07711 (Homo sapiens) Explore P07711 Go to UniProtKB: P07711
PHAROS: P07711 GTEx: ENSG00000135047
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07711
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ALD (Subject of Investigation/LOI) Query on ALD Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C]	E [auth A], H [auth B], J [auth C], L [auth D]	N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide C₂₆ H₄₃ N₃ O₅ WUJQMWDTZKIKQZ-VABKMULXSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D]	F [auth A] G [auth A] I [auth B] K [auth C] M [auth D] F [auth A], G [auth A], I [auth B], K [auth C], M [auth D], N [auth D], O [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain P [auth D] MOL2 format, chain P [auth D]	P [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001210 (ALD) Query on PRD_001210	E [auth A], H [auth B], J [auth C], L [auth D]	PHQ-Leu-Leu-Leu-aldehyde MG-132, bound form	Peptide-like / Inhibitor		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.198
R-Value Work: 0.180
R-Value Observed: 0.180
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.28	α = 105.536
b = 62.71	β = 93.388
c = 68.07	γ = 115.36

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-12-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Helmholtz Association	Slovenia	FISCOV
Helmholtz Association	Slovenia	SFragX
German Federal Ministry for Education and Research	Slovenia	16GW0277
German Federal Ministry for Education and Research	Slovenia	031B0405
Slovenian Research Agency	Slovenia	P1-0048
Slovenian Research Agency	Slovenia	IO-0048

Revision History (Full details and data files)

Version 1.0: 2022-12-28
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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Deposit Data

Help and Resources

7QKD

Crystal structure of human Cathepsin L in complex with covalently bound MG132

Sulfonated Calpeptin is a promising drug candidate against SARS-CoV-2 infections

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)