6VAH | pdb_00006vah

Crystal structure of human TEAD2 transcription factor in complex with Flufenamic acid derivative

PDB DOI: https://doi.org/10.2210/pdb6VAH/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-12-17 Released: 2020-04-15
Deposition Author(s): Halabelian, L., Zeng, H., Dong, A., Li, Y., Melin, L., Gagnon, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Santhakumar, V., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.242 (Depositor), 0.246 (DCC)
R-Value Work:
0.203 (Depositor), 0.210 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of human TEAD2 transcription factor in complex with Flufenamic acid derivative

Halabelian, L., Zeng, H., Dong, A., Li, Y., Melin, L., Gagnon, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Santhakumar, V., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 55.61 kDa
Atom Count: 3,238
Modeled Residue Count: 403
Deposited Residue Count: 480
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional enhancer factor TEF-4	A, B	240	Homo sapiens	Mutation(s): 0 Gene Names: TEAD2, TEF4
UniProt & NIH Common Fund Data Resources
Find proteins for Q15562 (Homo sapiens) Explore Q15562 Go to UniProtKB: Q15562
PHAROS: Q15562 GTEx: ENSG00000074219
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15562
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QZ1 (Subject of Investigation/LOI) Query on QZ1 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	2-fluoro-6-[(3-hexylphenyl)amino]benzoic acid C₁₉ H₂₂ F N O₂ QLXYHXDPYBBBIM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.242 (Depositor), 0.246 (DCC)
R-Value Work: 0.203 (Depositor), 0.210 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.792	α = 90
b = 61.307	β = 118.1
c = 79.862	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-04-15

Deposition Author(s):

Arrowsmith, C.H.

Santhakumar, V.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2020-04-15
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.