6IIU: Human thromboxane A2 receptor

Crystal structure of the human thromboxane A2 receptor bound to ramatroban. Determined by X-ray diffraction at 2.5 Å resolution. Released 19 Dec 2018.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Escherichia coli, Homo sapiens, Clostridium pasteurianum
Chains: 1
Atoms: 3,565
Mol. weight: 54.92 kDa
Ligands: OLC, CLR, ZN, A8X
Released: 19 Dec 2018

Explore 6IIU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6IIU contains 25 α-helices and 11 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: 25 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	1003-1019	17
α-helix	1023-1041	19
α-helix	1046-1048	3
α-helix	1056-1080	25
α-helix	1084-1092	9
α-helix	1094-1101	8
α-helix	1103-1105	3
α-helix	12-14	3
α-helix	19-25	7
α-helix	28-50	23
α-helix	62-90	29
α-helix	95-98	4
α-helix	103-135	33
α-helix	137-138	2
α-helix	143-164	22
α-helix	166-169	4
β-strand	174-177	4	1
β-strand	182-185	4	1
α-helix	191-225	35
β-strand	2004-2006	3	2
β-strand	2012-2013	2	2
β-strand	2019	1	3
α-helix	2020-2022	3
β-strand	2024	1	3
α-helix	2030-2032	3
β-strand	2038	1	4
β-strand	2045	1	4
α-helix	2046-2048	3
β-strand	2049-2051	3	2
α-helix	238-270	33
β-strand	276	1	5
α-helix	281	1
β-strand	282	1	5
α-helix	283	1
α-helix	284-310	27
α-helix	313-317	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562,Thromboxane A2 receptor,Rubredoxin,Thromboxane A2 receptor	A	protein	484	Escherichia coli, Homo sapiens, Clostridium pasteurianum	P00268 (AlphaFold model), P0ABE7 (AlphaFold model), P21731 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6IIU_1 Soluble cytochrome b562,Thromboxane A2 receptor,Rubredoxin,Thromboxane A2 receptor (chains A)
DYKDDDDGAPADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLED
KSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLPCFR
PTNITLEERRLIASPWFAASFCVVGLASNLLALSVLAGARQGGSHTRSSFLTFLCGLVLT
DFLGLLVTGTIVVSQHAALFEWHAVDPGCRLCRFMGVVMIFFGLSPLLLGAAMASERYLG
ITRPFSRPAVASQRRAWATVGLVWAAALALGLLPLLGVGRYTVQYPGSWCFLTLGAESGD
VAFGLLFSMLGGLSVGLSFLLNTVSVATLCHVYHGMKKYTCTVCGYIYNPEDGDPDNGVN
PGTDFKDIPDDWVCPLCGVGKDQFEEVEERDSEVEMMAQALGIMVVASVCWLPLLVFIAQ
TVLRNPPAMSPAGQLSRTTEKELLIYLRVATWNQILDPWVYILFRRAVLRRLQPRLEFLE
VLFQ

Ligands and cofactors

ID	Name	Formula	Copies
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	2
CLR	Cholesterol	C27 H46 O	1
ZN	Zinc ion	Zn	1
A8X	3-[(3R)-3-[(4-fluorophenyl)sulfonylamino]-1,2,3,4-tetrahydrocarbazol-9-yl]propa…	C21 H21 F N2 O4 S	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Structural basis for ligand recognition of the human thromboxane A2receptor. Fan, H., Chen, S., Yuan, X. et al. Nat Chem Biol (2019) 15:27-33. DOI 10.1038/s41589-018-0170-9 · PubMed

Other PDB entries of the same protein (UniProt P00268 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2PVE 0.79 Å, NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of…
1IRO 1.1 Å, Rubredoxin (oxidized, fe(iii)) at 1.1 Å resolution
1IRN 1.2 Å, Rubredoxin (ZN-substituted) at 1.2 Å resolution
4RXN 1.2 Å, Crystallographic refinement of rubredoxin at 1.2 Å resolution
5RXN 1.2 Å, Combined crystallographic refinement and energy minimization of rubredoxin at 1.2 Å…
1SMM 1.36 Å, Crystal Structure of Cp Rd L41A mutant in oxidized state
1SMW 1.38 Å, Crystal Structure of Cp Rd L41A mutant in reduced state 2 (soaked)
1SMU 1.43 Å, Crystal Structure of Cp Rd L41A mutant in reduced state 1 (drop-reduced)
1B13 1.5 Å, Clostridium pasteurianum rubredoxin G10A mutant
1FHH 1.5 Å, X-ray crystal structure of oxidized rubredoxin
1FHM 1.5 Å, X-ray crystal structure of reduced rubredoxin
1R0I 1.5 Å, cadmium-substituted rubredoxin

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