4XJJ | pdb_00004xjj

Extracellular domain of type II Transforming Growth Factor Beta receptor in complex with 2-(2-Hydroxyethyl)NDSB-201

PDB DOI: https://doi.org/10.2210/pdb4XJJ/pdb

Classification: Cytokine Receptor
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-01-08 Released: 2015-06-24
Deposition Author(s): Wangkanont, K., Forest, K.T., Kiessling, L.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.185 (Depositor), 0.186 (DCC)
R-Value Work:
0.153 (Depositor), 0.154 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Extracellular domain of type II Transforming Growth Factor Beta receptor in complex with 2-(2-Hydroxyethyl)NDSB-201

Wangkanont, K., Forest, K.T., Kiessling, L.L.

To be published.

Macromolecule Content

Total Structure Weight: 13 kDa
Atom Count: 1,023
Modeled Residue Count: 105
Deposited Residue Count: 112
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TGF-beta receptor type-2	A	112	Homo sapiens	Mutation(s): 1 Gene Names: TGFBR2 EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for P37173 (Homo sapiens) Explore P37173 Go to UniProtKB: P37173
PHAROS: P37173 GTEx: ENSG00000163513
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P37173
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
41D Query on 41D 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]	3-[2-(2-hydroxyethyl)pyridinium-1-yl]propane-1-sulfonate C₁₀ H₁₅ N O₄ S CBHRQLPSLPQVAZ-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: 0.185 (Depositor), 0.186 (DCC)
R-Value Work: 0.153 (Depositor), 0.154 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.17	α = 90
b = 40.373	β = 90
c = 76.341	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-06-24

Deposition Author(s):

Kiessling, L.L.

Revision History (Full details and data files)

Version 1.0: 2015-06-24
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
Version 1.2: 2024-11-06
Changes: 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.