9QKQ | pdb_00009qkq

Crystal structure of hTEAD4 YAP binding domain (hTEAD4-YBD) in complex with peptide 6

PDB DOI: https://doi.org/10.2210/pdb9QKQ/pdb

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

Deposited: 2025-03-20 Released: 2026-04-08
Deposition Author(s): Pozzi, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.221 (Depositor), 0.224 (DCC)
R-Value Work:
0.183 (Depositor), 0.188 (DCC)
R-Value Observed:
0.185 (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

Deciphering the structural and functional properties of interface 3 and lipidation pocket of hTEAD4 to develop new Hippo Pathway inhibitors through fluorescence anisotropy

Malpezzi, G., Scalvini, L., Tagliazucchi, L., Chiaravalle, A., Aiello, D., Saporito, G., Illuminati, D., Pacifico, S., Lopresti, L., Raucci, L., Guerrini, R., Pozzi, C., Venturelli, A., Ponterini, G., Mor, M., Costi, M.P.

To be published.

Macromolecule Content

Total Structure Weight: 56.88 kDa
Atom Count: 4,388
Modeled Residue Count: 454
Deposited Residue Count: 478
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional enhancer factor TEF-3	A, B	222	Homo sapiens	Mutation(s): 0 Gene Names: TEAD4, RTEF1, TCF13L1, TEF3
UniProt & NIH Common Fund Data Resources
Find proteins for Q15561 (Homo sapiens) Explore Q15561 Go to UniProtKB: Q15561
PHAROS: Q15561 GTEx: ENSG00000197905
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15561
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide 6	C, D	17	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MYR Query on MYR Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A]	F [auth A], O [auth B]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain O [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain P [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain P [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A] G [auth A] H [auth A] I [auth A] J [auth A] E [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
6CW Query on 6CW	C, D	L-PEPTIDE LINKING	C₁₁ H₁₁ Cl N₂ O₂		TRP
ALN Query on ALN	C, D	L-PEPTIDE LINKING	C₁₃ H₁₃ N O₂		ALA
NLE Query on NLE	C, D	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		LEU