6C1R: Human C5a receptor

Crystal structure of human C5a receptor in complex with an orthosteric antagonist PMX53 and an allosteric antagonist avacopan. Determined by X-ray diffraction at 2.2 Å resolution. Released 30 May 2018.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Escherichia coli, Homo sapiens, synthetic construct
Chains: 2
Atoms: 3,087
Mol. weight: 51.21 kDa
Ligands: OLA, OLC, MLI, EFD
Released: 30 May 2018

Explore 6C1R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6C1R contains 21 α-helices and 3 β-strands across 2 chains. 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 B: 21 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	13-27	15
α-helix	32-48	17
α-helix	69-90	22
α-helix	93-107	15
α-helix	118-120	3
α-helix	121-151	31
α-helix	156-172	17
α-helix	175-183	9
α-helix	192-197	6
α-helix	198-200	3
α-helix	201-225	25
α-helix	227-232	6
α-helix	236-259	24
β-strand	261-267	7	1
β-strand	270-276	7	1
α-helix	282-293	12
α-helix	294-298	5
α-helix	299-316	18
α-helix	324-352	29
α-helix	359-366	8
α-helix	368-375	8
α-helix	378-391	14
α-helix	401-409	9

Chain L: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-3	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562, C5a anaphylatoxin chemotactic receptor 1 chimera	B	protein	422	Escherichia coli, Homo sapiens	P0ABE7 (AlphaFold model), P21730 (AlphaFold model)
PMX53	L	protein	7	synthetic construct

Sequence of entity 1 (B), FASTA

>6C1R_1 Soluble cytochrome b562, C5a anaphylatoxin chemotactic receptor 1 chimera (chains B)
DYKDDDDVDADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDK
SPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLSNTLR
VPDILALVIFAVVFLVGVLGNALVVWVTAFEAKRTINAIWFLNLAVADFLSCLALPILFT
SIVQHHHWPFGGAACSILPSLILLNMYASILLLATISADRFLLVFKPIWCQNFRGAGLAW
IACAVAWGLALLLTIPSFLYRVVREEYFPPKVLCGVDYSHDKRRERAVAIVRLVLGFLWP
LLTLTICYTFILLRTWSRRATRSTKTLKVVVAVVASFFIFWLPYQVTGIMMSFLEPSSPT
FLLLKKLDSLCVSFAYINCCINPIIYVVAGQGFQGRLRKSLPSLLRNVLTEESVVRENLY
FQ

Sequence of entity 2 (L), FASTA

>6C1R_2 PMX53 (chains L)
XFAPAWR

Ligands and cofactors

ID	Name	Formula	Copies
OLA	Oleic acid	C18 H34 O2	4
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	2
MLI	Malonate ion	C3 H2 O4	2
EFD	avacopan	C33 H35 F4 N3 O2	1

Water and common crystallization additives (PGE, NA) are not listed.

Primary citation

Orthosteric and allosteric action of the C5a receptor antagonists. Liu, H., Kim, H.R., Deepak, R.N.V.K. et al. Nat Struct Mol Biol (2018) 25:472-481. DOI 10.1038/s41594-018-0067-z · 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

Browse structure collections

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