3V2Y: Lipid G protein-Coupled Receptor

Crystal Structure of a Lipid G protein-Coupled Receptor at 2.80A. Determined by X-ray diffraction at 2.8 Å resolution. Released 15 Feb 2012.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, Enterobacteria phage T4
Chains: 1
Atoms: 3,523
Mol. weight: 59.54 kDa
Ligands: NAG, ML5
Released: 15 Feb 2012

Explore 3V2Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V2Y contains 24 α-helices and 7 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 24 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	23-32	10
α-helix	36-39	4
α-helix	42-72	31
α-helix	79-104	26
α-helix	106-109	4
α-helix	114-146	33
α-helix	158-176	19
β-strand	183	1	1
α-helix	188-190	3
β-strand	191	1	2
β-strand	198	1	1
β-strand	199	1	2
α-helix	200-1010	41
β-strand	1018-1019	2	3
β-strand	1025-1027	3	3
β-strand	1031-1032	2	3
α-helix	1039-1050	12
α-helix	1060-1078	19
α-helix	1085-1090	6
α-helix	1093-1105	13
α-helix	1108-1112	5
α-helix	1115-1122	8
α-helix	1126-1135	10
α-helix	1137-1141	5
α-helix	1143-1155	13
α-helix	1158-1160	3
α-helix	251-280	30
α-helix	294-302	9
α-helix	303-305	3
α-helix	307-314	8
α-helix	316-323	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sphingosine 1-phosphate receptor 1, Lysozyme chimera (E.C.3.2.1.17)	A	protein	520	Homo sapiens, Enterobacteria phage T4	P00720, P21453 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3V2Y_1 Sphingosine 1-phosphate receptor 1, Lysozyme chimera (E.C.3.2.1.17) (chains A)
MKTIIALSYIFCLVFAGAPGPTSVPLVKAHRSSVSDYVNYDIIVRHYNYTGKLNISADKE
NSIKLTSVVFILICCFIILENIFVLLTIWKTKKFHRPMYYFIGNLALSDLLAGVAYTANL
LLSGATTYKLTPAQWFLREGSMFVALSASVFSLLAIAIERYITMLKMKLHNGSNNFRLFL
LISACWVISLILGGLPIMGWNCISALSSCSTVLPLYHKHYILFCTTVFTLLLLSIVILYC
RIYSLVRTRNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGR
NTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVA
GFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYASRSSENVALL
KTVIIVLSVFIACWAPLFILLLLDVGCKVKTCDILFRAEYFLVLAVLNSGTNPIIYTLTN
KEMRRAFIRIMGRPLEVLFQGPHHHHHHHHHHDYKDDDDK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
ML5	{(3R)-3-amino-4-[(3-hexylphenyl)amino]-4-oxobutyl}phosphonic acid	C16 H27 N2 O4 P	1

Primary citation

Crystal structure of a lipid G protein-coupled receptor. Hanson, M.A., Roth, C.B., Jo, E. et al. Science (2012) 335:851-855. DOI 10.1126/science.1215904 · PubMed

Other PDB entries of the same protein (UniProt P00720), best resolution first:

2O7A 0.84 Å, T4 lysozyme C-terminal fragment
5JDT 1.0 Å, Structure of Spin-labelled T4 lysozyme mutant L118C-R1 at 100K
7LOE 1.01 Å, T4 lysozyme mutant L99A in complex with 1-fluoranylnaphthalene
7LOD 1.02 Å, T4 lysozyme mutant L99A in complex with 1-fluoranyl-4-iodanyl-benzene
7LX8 1.03 Å, T4 lysozyme mutant L99A
5XPF 1.04 Å, High-resolution X-ray structure of the T26H mutant of T4 lysozyme
6BG3 1.05 Å, Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl…
7LOF 1.05 Å, T4 lysozyme mutant L99A in complex with 2-butylthiophene
7LX6 1.05 Å, T4 lysozyme mutant L99A
7LX7 1.05 Å, T4 lysozyme mutant L99A
1SWY 1.06 Å, Use of a Halide Binding Site to Bypass the 1000-atom Limit to Ab initio Structure…
1SWZ 1.06 Å, Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure…

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