6ZU8 | pdb_00006zu8

Crystal structure of human Brachyury G177D variant in complex with Afatinib

PDB DOI: https://doi.org/10.2210/pdb6ZU8/pdb

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

Deposited: 2020-07-21 Released: 2020-08-05
Deposition Author(s): Newman, J.A., Gavard, A.E., Shrestha, L., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Gileadi, O.
Funding Organization(s): The Mark Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.260 (Depositor), 0.261 (DCC)
R-Value Work:
0.218 (Depositor), 0.218 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of human Brachyury G177D variant in complex with Afatinib

Newman, J.A., Gavard, A.E., Shrestha, 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: 22.63 kDa
Atom Count: 1,531
Modeled Residue Count: 179
Deposited Residue Count: 192
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Brachyury protein	A	192	Homo sapiens	Mutation(s): 0
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0WN (Subject of Investigation/LOI) Query on 0WN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	N-{4-[(3-chloro-4-fluorophenyl)amino]-7-[(3S)-tetrahydrofuran-3-yloxy]quinazolin-6-yl}-4-(dimethylamino)butanamide C₂₄ H₂₇ Cl F N₅ O₃ JSENTLOBWVHLNR-INIZCTEOSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-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: 1.95 Å
R-Value Free: 0.260 (Depositor), 0.261 (DCC)
R-Value Work: 0.218 (Depositor), 0.218 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.107	α = 90
b = 49.269	β = 90
c = 83.74	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-08-05

Deposition Author(s):

Funding Organization	Location	Grant Number
The Mark Foundation	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2020-08-05
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-09
Changes: Structure summary