5D5A

In meso in situ serial X-ray crystallography structure of the Beta2-adrenergic receptor at 100 K

PDB DOI: https://doi.org/10.2210/pdb5D5A/pdb

Classification: Membrane Protein/Hydrolase
Organism(s): Homo sapiens, Tequatrovirus T4
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2015-08-10 Released: 2016-01-13
Deposition Author(s): Huang, C.-Y., Olieric, V., Warshamanage, R., Liu, X., Kobilka, B., Kay Diederichs, K., Wang, M., Caffrey, M.
Funding Organization(s): Science Foundation Ireland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.262
R-Value Work: 0.212
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 60.02 kDa
Atom Count: 3,809
Modelled Residue Count: 442
Deposited Residue Count: 500
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2 adrenergic receptor,Endolysin,Beta-2 adrenergic receptor	A	500	Homo sapiens, Tequatrovirus T4	Mutation(s): 3 Gene Names: ADRB2, ADRB2R, B2AR EC: 3.2.1.17 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P07550 (Homo sapiens) Explore P07550 Go to UniProtKB: P07550
PHAROS: P07550 GTEx: ENSG00000169252
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720 Go to UniProtKB: P00720
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P00720P07550
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G66120GK GlyCosmos: G66120GK

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
12P Query on 12P Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	DODECAETHYLENE GLYCOL C₂₄ H₅₀ O₁₃ WRZXKWFJEFFURH-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A]	G [auth A], H [auth A], I [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
CAU Query on CAU Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	(2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol C₁₈ H₂₂ N₂ O₂ BQXQGZPYHWWCEB-ZDUSSCGKSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain M [auth A]	L [auth A] M [auth A] N [auth A] O [auth A] P [auth A] L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
BU1 Query on BU1 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	1,4-BUTANEDIOL C₄ H₁₀ O₂ WERYXYBDKMZEQL-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
ACM Query on ACM Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	ACETAMIDE C₂ H₅ N O DLFVBJFMPXGRIB-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900018 Query on PRD_900018	B	beta-maltose	Oligosaccharide / Nutrient		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.262
R-Value Work: 0.212
R-Value Observed: 0.214
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107	α = 90
b = 170	β = 106.25
c = 40.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-01-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Science Foundation Ireland	Ireland	12/IA/1255

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 1.1: 2016-03-02
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary

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5D5A

In meso in situ serial X-ray crystallography structure of the Beta2-adrenergic receptor at 100 K

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2