8CN6: CD59

CD59 in complex with CP-06 peptide. Determined by X-ray diffraction at 2.43 Å resolution. Released 13 Nov 2024.

Method: X-ray diffraction
Resolution: 2.43 Å
Organisms: Homo sapiens, synthetic construct
Chains: 9
Atoms: 4,063
Mol. weight: 59.11 kDa
Ligands: ZN
Released: 13 Nov 2024

Explore 8CN6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CN6 contains 18 α-helices and 36 β-strands across 9 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: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
β-strand	16-19	4	1
β-strand	25-31	7	2
β-strand	34-40	7	2
α-helix	42-44	3
α-helix	47-54	8
β-strand	60-64	5	2
α-helix	72-74	3

Chain B: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
β-strand	15-18	4	1
β-strand	25-31	7	3
β-strand	34-40	7	3
α-helix	42-44	3
α-helix	47-54	8
β-strand	60-64	5	3
α-helix	72-74	3

Chains C, D and E: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	4
β-strand	16-18	3	4
β-strand	25-31	7	2
β-strand	34-40	7	2
α-helix	42-44	3
α-helix	47-54	8
β-strand	60-64	5	2
α-helix	72-74	3

Chain F: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	1-4	4	8
β-strand	16-19	4	8
β-strand	25-31	7	6
β-strand	34-40	7	6
α-helix	42-44	3
α-helix	47-54	8
β-strand	60-64	5	6
α-helix	72-74	3

Chain G: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	2
β-strand	11-14	4	2

Chain H: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	11-14	4	6

Chain J: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	3
β-strand	13-14	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CD59 glycoprotein	A, B, C, D, E, F	protein	77	Homo sapiens	P13987 (AlphaFold model)
Cyclic peptide CP-06	G, H, J	protein	16	synthetic construct

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>8CN6_1 CD59 glycoprotein (chains A, B, C, D, E, F)
MLQCYNCPNPTADCKTAVNCSSDFDACLITKAGLQVYNKCWKFEHCNFNDVTTRLRENEL
TYYCCKKDLCNFNEQLE

Sequence of entity 2 (G, H, J), FASTA

>8CN6_2 Cyclic peptide CP-06 (chains G, H, J)
XYSWTWGNRSSVRGCX

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Macrocyclic Peptide Probes for Immunomodulatory Protein CD59: Potent Modulators of Bacterial Toxin Activity and Antibody-Dependent Cytotoxicity. Bickel, J.K., Ahmed, A.I.S., Pidd, A.B. et al. Angew Chem Int Ed Engl (2025):e202422673-e202422673. DOI 10.1002/anie.202422673 · PubMed

Other PDB entries of the same protein (UniProt P13987 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2J8B 1.15 Å, High resolution structure of human CD59
2UWR 1.34 Å, High resolution structure of human CD59
2UX2 1.8 Å, High resolution structure of human CD59
2OFS 2.12 Å, Crystal structure of human CD59
5IMY 2.4 Å, Trapped Toxin
5IMT 2.7 Å, Toxin receptor complex
8B0F 3.0 Å, CryoEM structure of C5b8-CD59
8B0G 3.3 Å, 2C9, C5b9-CD59 structure
8B0H 3.3 Å, 2C9, C5b9-CD59 cryoEM structure
4BIK 3.49 Å, Structure of a disulfide locked mutant of Intermedilysin with human CD59
6ZD0 4.6 Å, Disulfide-locked early prepore intermedilysin-CD59
1CDQ Structure of a soluble, glycosylated form of the human complement regulatory protein CD59

Browse structure collections

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