5QT0 | pdb_00005qt0

PanDDA analysis group deposition -- Crystal Structure of human Brachyury G177D variant in complex with Z321318226

PDB DOI: https://doi.org/10.2210/pdb5QT0/pdb
Deposition Group: G_1002086 (changed state) | Explore G_1002086

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-05-26 Released: 2019-08-21
Deposition Author(s): Newman, J.A., Gavard, A.E., Sherestha, L., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.257 (Depositor), 0.272 (DCC)
R-Value Work:
0.186 (Depositor), 0.206 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

PanDDA analysis group deposition

Newman, J.A., Gavard, A.E., Sherestha, L., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

To be published.

Macromolecule Content

Total Structure Weight: 19.9 kDa
Atom Count: 1,681
Modeled Residue Count: 171
Deposited Residue Count: 172
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-box transcription factor T	A	172	Homo sapiens	Mutation(s): 1 Gene Names: TBXT, T
UniProt & NIH Common Fund Data Resources
Find proteins for O15178 (Homo sapiens) Explore O15178 Go to UniProtKB: O15178
PHAROS: O15178 GTEx: ENSG00000164458
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15178
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JHJ (Subject of Investigation/LOI) Query on JHJ Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-(4-methoxyphenyl)-N'-pyridin-4-ylurea C₁₃ H₁₃ N₃ O₂ IFKGCTGEAFOLOL-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.257 (Depositor), 0.272 (DCC)
R-Value Work: 0.186 (Depositor), 0.206 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.93	α = 90
b = 99.93	β = 90
c = 98.02	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-08-21

Deposition Author(s):

Burgess-Brown, N.A.

Arrowsmith, C.H.

Revision History (Full details and data files)

Version 1.0: 2019-08-21
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references
Version 1.2: 2026-02-18
Changes: Refinement description, Structure summary

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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.