6C1Q: Human C5a receptor

Crystal structure of human C5a receptor in complex with an orthosteric antagonist PMX53 and an allosteric antagonist NDT9513727. Determined by X-ray diffraction at 2.9 Å resolution. Released 30 May 2018.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Escherichia coli, Homo sapiens, synthetic construct
Chains: 2
Atoms: 2,918
Mol. weight: 48.98 kDa
Ligands: 9P2
Released: 30 May 2018

Explore 6C1Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6C1Q contains 19 α-helices and 4 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: 19 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	12-27	16
α-helix	32-48	17
α-helix	65-90	26
α-helix	93-113	21
α-helix	121-150	30
α-helix	156-172	17
α-helix	175-183	9
β-strand	187	1	1
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	359-376	18
α-helix	378-391	14
α-helix	401-408	8

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

>6C1Q_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

>6C1Q_2 PMX53 (chains L)
XFAPAWR

Ligands and cofactors

ID	Name	Formula	Copies
9P2	1-(1,3-benzodioxol-5-yl)-~{N}-(1,3-benzodioxol-5-ylmethyl)-~{N}-[(3-butyl-2,5-d…	C36 H35 N3 O4	1

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

About this viewer

MolViewer shows 6C1Q directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.