5QRR | pdb_00005qrr

PanDDA analysis group deposition -- Crystal Structure of human Brachyury in complex with Z31720228

• PDB DOI: https://doi.org/10.2210/pdb5QRR/pdb
• Deposition Group: G_1002080 (changed state) | Explore  G_1002080  

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


• Deposited: 2019-05-25 Released: 2019-07-10 
• Deposition Author(s): Newman, J.A., Gavard, A.E., Fernandez-Cid, A., Sherestha, L., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.272 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

PanDDA analysis group deposition

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 20.39 kDa 
• Atom Count: 1,469 
• Modeled Residue Count: 171 
• Deposited Residue Count: 172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-box transcription factor T	A	172	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NY1 (Subject of Investigation/LOI)	G [auth A]	2-(2-methyl-1,3-thiazol-4-yl)-1-(morpholin-4-yl)ethan-1-one C10 H14 N2 O2 S ZGUYZZRXRYNXNN-UHFFFAOYSA-N
CD	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.272 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.924	α = 90
b = 59.924	β = 90
c = 109.985	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Newman, J.A., Gavard, A.E., Fernandez-Cid, A., Sherestha, L., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2019-08-07
  Changes: Author supporting evidence, Data collection, Structure summary
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2026-02-18
  Changes: Refinement description, Structure summary