8YHF | pdb_00008yhf

The Crystal Structure of the Type I TGF beta receptor from Biortus.

PDB DOI: https://doi.org/10.2210/pdb8YHF/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-02-28 Released: 2024-03-13
Deposition Author(s): Wang, F., Cheng, W., Lv, Z., Meng, Q., Xu, Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.192 (Depositor), 0.203 (DCC)
R-Value Work:
0.166 (Depositor), 0.176 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

The Crystal Structure of the Type I TGF beta receptor from Biortus.

Wang, F., Cheng, W., Lv, Z., Meng, Q., Xu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 39.38 kDa
Atom Count: 2,847
Modeled Residue Count: 298
Deposited Residue Count: 343
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TGF-beta receptor type-1	A	343	Homo sapiens	Mutation(s): 0 Gene Names: TGFBR1, ALK5, SKR4 EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for P36897 (Homo sapiens) Explore P36897 Go to UniProtKB: P36897
PHAROS: P36897 GTEx: ENSG00000106799
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36897
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D6I (Subject of Investigation/LOI) Query on A1D6I 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]	Vactosertib C₂₂ H₁₈ F N₇ FJCDSQATIJKQKA-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: 1.40 Å
R-Value Free: 0.192 (Depositor), 0.203 (DCC)
R-Value Work: 0.166 (Depositor), 0.176 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.196	α = 90
b = 76.764	β = 90
c = 89.707	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	China	--

Revision History (Full details and data files)

Version 1.0: 2024-03-13
Type: Initial release
Version 1.1: 2024-11-20
Changes: Derived calculations, 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.