4Z34: Human Lysophosphatidic Acid Receptor 1

Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO9780307. Determined by X-ray diffraction at 3.0 Å resolution. Released 3 Jun 2015.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 1
Atoms: 3,047
Mol. weight: 53.44 kDa
Ligands: ON7, 1WV
Released: 3 Jun 2015

Explore 4Z34 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Z34 contains 16 α-helices and 2 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: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	29-36	8
α-helix	47-76	30
α-helix	78-80	3
α-helix	83-106	24
α-helix	110-113	4
α-helix	118-149	32
α-helix	158-178	21
α-helix	181-183	3
α-helix	192-194	3
β-strand	195	1	1
β-strand	203	1	1
α-helix	204-1018	47
α-helix	1023-1039	17
α-helix	1059-1081	23
α-helix	1084-1105	22
α-helix	250-283	34
α-helix	294-314	21
α-helix	316-326	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysophosphatidic acid receptor 1, Soluble cytochrome b562	A	protein	464	Homo sapiens, Escherichia coli	P0ABE7 (AlphaFold model), Q92633 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4Z34_1 Lysophosphatidic acid receptor 1, Soluble cytochrome b562 (chains A)
MKTIIALSYIFCLVFAGAPAAISTSIPVISQPQFTAMNEPQCFYNESIAFFYNRSGKHLA
TEWNTVSKLVMGLGITVCIFIMLANLLVMVAIYVNRRFHFPIYYLMANLAAADFFAGLAY
FYLMFNTGPNTRRLTVSTWLLRQGLIDTSLTASVANLLAIAIERHITVFRMQLHTRMSNR
RVVVVIVVIWTMAIVMGAIPSVGWNCICDIENCSNMAPLYSDSYLVFWAIFNLVTFVVMV
VLYAHIFGYVADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLED
KSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLRNRD
TMMSLLKTVVIVLGAFIICWTPGLVLLLLDVCCPQCDVLAYEKFFLLLAEFNSAMNPIIY
SYRDKEMSATFRQILGRPLEVLFQGPHHHHHHHHHHDYKDDDDK

Ligands and cofactors

ID	Name	Formula	Copies
ON7	{1-[(2S,3S)-2-(2,3-dihydro-1H-inden-2-ylmethyl)-3-(3,5-dimethoxy-4-methylphenyl…	C30 H35 N O7	1
1WV	(2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate	C17 H32 O4	1

Primary citation

Crystal Structure of Antagonist Bound Human Lysophosphatidic Acid Receptor 1. Chrencik, J.E., Roth, C.B., Terakado, M. et al. Cell (2015) 161:1633-1643. DOI 10.1016/j.cell.2015.06.002 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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