7QNS | pdb_00007qns

Peptide VYEKKP in complex with human cathepsin V C25S mutant

PDB DOI: https://doi.org/10.2210/pdb7QNS/pdb

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

Deposited: 2021-12-22 Released: 2023-01-18
Deposition Author(s): Loboda, J., Sosnowski, P., Tusar, L., Vidmar, R., Vizovisek, M., Horvat, J., Kosec, G., Impens, F., Demol, H., Turk, B., Gevaert, K., Turk, D.
Funding Organization(s): Slovenian Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.201 (Depositor), 0.183 (DCC)
R-Value Work:
0.177 (Depositor), 0.178 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Peptide VYEKKP in complex with human cathepsin V C25S mutant

Loboda, J., Sosnowski, P., Tusar, L., Vidmar, R., Vizovisek, M., Horvat, J., Kosec, G., Impens, F., Demol, H., Turk, B., Gevaert, K., Turk, D.

To be published.

Macromolecule Content

Total Structure Weight: 51.83 kDa
Atom Count: 3,987
Modeled Residue Count: 455
Deposited Residue Count: 462
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin L2	A [auth AA], B [auth BA]	222	Homo sapiens	Mutation(s): 3 Gene Names: CTSV, CATL2, CTSL2, CTSU, UNQ268/PRO305 EC: 3.4.22.43
UniProt & NIH Common Fund Data Resources
Find proteins for O60911 (Homo sapiens) Explore O60911 Go to UniProtKB: O60911
PHAROS: O60911 GTEx: ENSG00000136943
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60911
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VAL-TYR-GLU-LYS-LYS-PRO	C [auth PC], D [auth PB], E [auth PA]	6	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain R [auth BA] SDF format, chain Q [auth BA] SDF format, chain P [auth BA] SDF format, chain N [auth BA] SDF format, chain M [auth BA] SDF format, chain I [auth AA] MOL2 format, chain R [auth BA] MOL2 format, chain Q [auth BA] MOL2 format, chain P [auth BA] MOL2 format, chain N [auth BA] MOL2 format, chain M [auth BA] MOL2 format, chain I [auth AA] mmCIF format, chain R [auth BA] mmCIF format, chain Q [auth BA] mmCIF format, chain P [auth BA] mmCIF format, chain N [auth BA] mmCIF format, chain M [auth BA] mmCIF format, chain I [auth AA]	I [auth AA] M [auth BA] N [auth BA] P [auth BA] Q [auth BA] I [auth AA], M [auth BA], N [auth BA], P [auth BA], Q [auth BA], R [auth BA]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain I [auth AA] Focus chain M [auth BA] Focus chain N [auth BA] Focus chain P [auth BA] Focus chain Q [auth BA] Focus chain R [auth BA] Interactions & Density Focus chain I [auth AA] Focus chain M [auth BA] Focus chain N [auth BA] Focus chain P [auth BA] Focus chain Q [auth BA] Focus chain R [auth BA]
TFA Query on TFA Download:Ideal Coordinates CCD File SDF format, chain J [auth AA] SDF format, chain H [auth AA] MOL2 format, chain J [auth AA] MOL2 format, chain H [auth AA] mmCIF format, chain J [auth AA] mmCIF format, chain H [auth AA]	H [auth AA], J [auth AA]	trifluoroacetic acid C₂ H F₃ O₂ DTQVDTLACAAQTR-UHFFFAOYSA-N		Interactions Focus chain H [auth AA] Focus chain J [auth AA] Interactions & Density Focus chain H [auth AA] Focus chain J [auth AA]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth BA] SDF format, chain G [auth AA] MOL2 format, chain O [auth BA] MOL2 format, chain G [auth AA] mmCIF format, chain O [auth BA] mmCIF format, chain G [auth AA]	G [auth AA], O [auth BA]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth AA] Focus chain O [auth BA] Interactions & Density Focus chain G [auth AA] Focus chain O [auth BA]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth BA] SDF format, chain K [auth AA] SDF format, chain F [auth AA] MOL2 format, chain L [auth BA] MOL2 format, chain K [auth AA] MOL2 format, chain F [auth AA] mmCIF format, chain L [auth BA] mmCIF format, chain K [auth AA] mmCIF format, chain F [auth AA]	F [auth AA], K [auth AA], L [auth BA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth AA] Focus chain K [auth AA] Focus chain L [auth BA] Interactions & Density Focus chain F [auth AA] Focus chain K [auth AA] Focus chain L [auth BA]