8A5B

Crystal structure of human cathepsin L in complex with covalently bound MG-101

PDB DOI: https://doi.org/10.2210/pdb8A5B/pdb

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

Deposited: 2022-06-14 Released: 2023-07-05
Deposition Author(s): Falke, S., Lieske, J., Guenther, S., Reinke, P.Y.A., Ewert, W., Loboda, J., Karnicar, K., Usenik, A., Lindic, N., Sekirnik, A., Chapman, H.N., Hinrichs, W., 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: 1.80 Å
R-Value Free: 0.225
R-Value Work: 0.178
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Structural elucidation of antiviral cathepsin L inhibitors

Falke, S., Lieske, J., Herrmann, A., Guenther, S., Reinke, P.Y.A., Ewert, W., Loboda, J., Karnicar, K., Usenik, A., Lindic, N., Sekirnik, A., Chapman, H.N., Hinrichs, W., Ebert, G., Turk, D., Meents, A.

To be published.

Macromolecule Content

Total Structure Weight: 98.75 kDa
Atom Count: 7,216
Modelled Residue Count: 892
Deposited Residue Count: 896
Unique protein chains: 2

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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calpain Inhibitor I	E, F, G, H	4	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain N [auth D] SDF format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D]	M [auth C], N [auth D], O [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain P [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain P [auth D]	J [auth A], K [auth B], L [auth B], P [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth D] Interactions & Density Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] 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_002460 Query on PRD_002460	E, F, G, H		Peptide-like / Inhibitor		Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.225
R-Value Work: 0.178
R-Value Observed: 0.179
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.24	α = 105.349
b = 62.2	β = 93.245
c = 67.24	γ = 115.807

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-05

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

Revision History (Full details and data files)

Version 1.0: 2023-07-05
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection
Version 2.1: 2024-02-07
Changes: Refinement description

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Help and Resources

8A5B

Crystal structure of human cathepsin L in complex with covalently bound MG-101

Structural elucidation of antiviral cathepsin L inhibitors

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2