9Y6C: Complement C5

X-ray structure analysis of human Complement Component 5 TE domain in complex with the peptide Ra30303. Determined by X-ray diffraction at 2.0 Å resolution. Released 24 Dec 2025.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 2,800
Mol. weight: 38.66 kDa
Ligands: 8VH
Released: 24 Dec 2025

Explore 9Y6C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Y6C contains 15 α-helices and 9 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 A: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	985-992	8
α-helix	1008-1027	20
α-helix	1038-1057	20
β-strand	1060	1	1
β-strand	1066	1	1
β-strand	1067	1	2
β-strand	1074	1	2
α-helix	1076-1089	14
α-helix	1097-1111	15
β-strand	1112	1	3
β-strand	1118	1	3
α-helix	1136-1155	20
α-helix	1156-1158	3
α-helix	1162-1178	17
α-helix	1185-1196	12
α-helix	1203-1213	11
β-strand	1217-1219	3	4
β-strand	1225-1227	3	4
α-helix	1245-1260	16
α-helix	1264-1277	14
α-helix	1278-1279	2
α-helix	1287-1304	18

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	9-11	3	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C5	A	protein	324	Homo sapiens	P01031 (AlphaFold model)
peptide Ra30303	B	protein	17	synthetic construct

Sequence of entity 1 (A), FASTA

>9Y6C_1 Complement C5 (chains A)
LLVGEILSAVLSQEGINILTHLPKGSAEAELMSVVPVFYVFHYLETGNHWNIFHSDPLIE
KQKLKKKLKEGMLSIMSYRNADYSYSVWKGGSASTWLTAFALRVLGQVNKYVEQNQNSIC
NSLLWLVENYQLDNGSFKENSQYQPIKLQGTLPVEARENSLYLTAFTVIGIRKAFDICPL
VKIDTALIKADNFLLENTLPAQSTFTLAISAYALSLGDKTHPQFRSIVSALKREALVKGN
PPIYRFWKDNLQHKDSSVPNTGTARMVETTAYALLTSLNLKDINYVNPVIKWLSEEQRYG
GGFYSTQDTINAIEGLTEYSLLVK

Sequence of entity 2 (B), FASTA

>9Y6C_2 peptide Ra30303 (chains B)
XCVERFCDVYWEYPAVX

Ligands and cofactors

ID	Name	Formula	Copies
8VH	1,3-dimethylbenzene	C8 H10	1

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

Primary citation

Discovery of Zilucoplan: A Complement C5 Inhibitor for Treatment of Anti-Acetylcholine Receptor (AChR) Antibody-Positive Generalized Myasthenia Gravis (gMG). Ye, P., Hammer, R.P., Wang, Z. et al. J Med Chem (2025) 68:25772-25782. DOI 10.1021/acs.jmedchem.5c02537 · PubMed

Other PDB entries of the same protein (UniProt P01031 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5B71 2.11 Å, Crystal structure of complement C5 in complex with SKY59
4UU9 2.12 Å, Crystal structure of the human c5a in complex with MEDI7814 a neutralising antibody
7AD7 2.3 Å, Crystal structure of human complement C5 in complex with the K8 bovine knob domain…
5B4P 2.4 Å, Complex structure of human C5a and its binding repebody
4P39 2.4 Å, Crystal structure of the human C5aR antagonist C5a-A8
7OP0 2.57 Å, Crystal structure of complement C5 in complex with chemically synthesized K92 knob domain.
3HQA 2.59 Å, Crystal structure of human desarg-C5A
5HCC 2.59 Å, Ternary complex of human Complement C5 with Ornithodoros moubata OmCI and Dermacentor…
22GM 2.7 Å, C5a bound C5aR1 in complex with beta-arrestin1
6RPT 2.7 Å, Structure of tick complement inhibitor CirpT1 complexed with macroglobubulin domain 4 of…
7AD6 2.75 Å, Crystal structure of human complement C5 in complex with the K92 bovine knob domain…
22GK 2.84 Å, C5a bound C5aR2 in complex with beta-arrestin1

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