8YPA | pdb_00008ypa

Human mitochondrial ClpP in complex with TR89

PDB DOI: https://doi.org/10.2210/pdb8YPA/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-16 Released: 2025-03-19
Deposition Author(s): Li, Q.-N., Sun, H.-Y., Xiao, Y.-B.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.67 Å
R-Value Free:
0.258 (Depositor), 0.256 (DCC)
R-Value Work:
0.215 (Depositor), 0.214 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Human mitochondrial ClpP in complex with TR89

Li, Q.-N., Sun, H.-Y., Xiao, Y.-B.

To be published.

Macromolecule Content

Total Structure Weight: 173.53 kDa
Atom Count: 9,773
Modeled Residue Count: 1,248
Deposited Residue Count: 1,561
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit, mitochondrial	A, B, C, D, E A, B, C, D, E, F, G	223	Homo sapiens	Mutation(s): 0 Gene Names: CLPP EC: 3.4.21.92
UniProt & NIH Common Fund Data Resources
Find proteins for Q16740 (Homo sapiens) Explore Q16740 Go to UniProtKB: Q16740
PHAROS: Q16740 GTEx: ENSG00000125656
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16740
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1LZN (Subject of Investigation/LOI) Query on A1LZN Download:Ideal Coordinates CCD File SDF format, chain N [auth G] SDF format, chain M [auth F] SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth B] SDF format, chain H [auth A] MOL2 format, chain N [auth G] MOL2 format, chain M [auth F] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] mmCIF format, chain N [auth G] mmCIF format, chain M [auth F] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A]	H [auth A] I [auth B] J [auth C] K [auth D] L [auth D] H [auth A], I [auth B], J [auth C], K [auth D], L [auth D], M [auth F], N [auth G]	(6~{R})-2-[[3,5-bis(fluoranyl)phenyl]methyl]-6-(hydroxymethyl)-5-[[4-(trifluoromethyl)phenyl]methyl]-7,8-dihydro-6~{H}-pyrazolo[1,5-a][1,4]diazepin-4-one C₂₃ H₂₀ F₅ N₃ O₂ SZLZNFDCRGBJIA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth F] Focus chain N [auth G] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth F] Focus chain N [auth G]