3V2W

Crystal Structure of a Lipid G protein-Coupled Receptor at 3.35A

PDB DOI: https://doi.org/10.2210/pdb3V2W/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens, Tequatrovirus T4
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2011-12-12 Released: 2012-02-15
Deposition Author(s): Hanson, M.A., Roth, C.B., Jo, E., Griffith, M.T., Scott, F.L., Reinhart, G., Desale, H., Clemons, B., Cahalan, S.M., Schuerer, S.C., Sanna, M.G., Han, G.W., Kuhn, P., Rosen, H., Stevens, R.C., GPCR Network (GPCR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free: 0.281
R-Value Work: 0.224
R-Value Observed: 0.228

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 59.54 kDa
Atom Count: 3,423
Modelled Residue Count: 442
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sphingosine 1-phosphate receptor 1, Lysozyme chimera	A	520	Homo sapiens, Tequatrovirus T4	Mutation(s): 2 Gene Names: S1PR1, CHEDG1, EDG1 EC: 3.2.1.17 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P21453 (Homo sapiens) Explore P21453 Go to UniProtKB: P21453
PHAROS: P21453 GTEx: ENSG00000170989
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	P00720P21453
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ML5 Query on ML5 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	{(3R)-3-amino-4-[(3-hexylphenyl)amino]-4-oxobutyl}phosphonic acid C₁₆ H₂₇ N₂ O₄ P FWJRVGZWNDOOFH-OAHLLOKOSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
ML5	PDBBind: 3V2W	Ki: 77 (nM) from 1 assay(s)
ML5	BindingDB: 3V2W	Ki: min: 18, max: 77 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free: 0.281
R-Value Work: 0.224
R-Value Observed: 0.228
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.94	α = 90
b = 69.7	β = 90
c = 81.93	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
BUSTER	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-02-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-15
Type: Initial release
Version 1.1: 2012-03-14
Changes: Database references
Version 1.2: 2017-06-21
Changes: Data collection, Database references, Source and taxonomy, Structure summary
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2024-04-03
Changes: Data collection, Database references, Refinement description, Structure summary

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3V2W

Crystal Structure of a Lipid G protein-Coupled Receptor at 3.35A

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)