Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5869 |
| PDBID: | 8CDD |
| Chains: | ED_B |
| Organism: | Plasmodium falciparum 3D7, Gallus gallus |
| Method: | EM |
| Resolution (Å): | 3.00 |
| Reference: | 10.1038/s41586-023-06856-1 |
| Antibody | |
| Antibody: | Cy.003 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Plasmodium falciparum 3D7 cysteine-rich protective antigen (PfCyRPA) |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: E
Mutation: NULL
| >8CDD_E|Chain E|Cy.003 heavy chain|Gallus gallus (9031) AVTLDESGGGLQTPGGALSLVCKGSGFFSFSSYTMQWVRQAPGKGLEWVASISSGGGTNYGAAVKGRATISRDNGQSTLRLQLNNLRAEDTGTYYCAKHGVNGCDWSYSVGCVDAWGHGTEVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP |
Light Chain: D
Mutation: NULL
| >8CDD_D|Chain D|Cy.003 light chain|Gallus gallus (9031) ALTQPSSVSANPGETVKITCSGGSSSYYGWYQQKSPGSAPVTLIYNNQKRPSDIPSRFSGSKSGSTGTLTITGVQAEDEAVYFCGSRDNSGGIFGAGTTLTVLRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR |
Antigen
Chain: B
Mutation: NULL
| >8CDD_B|Chain B|Cysteine-rich protective antigen|Plasmodium falciparum 3D7 (36329) DSRHVFIRTELSFIKNNVPCIRDMFFIYKRELYNICLDDLKGEEDETHIYVQKKVKDSWITLNDLFKETDLTGRPHIFAYVDVEEIIILLCEDEEFSNRKKDMTCHRFYSNDGKEYNNAEITISDYILKDKLLSSYVSLPLKIENREYFLICGVSPYKFKDDNKKDDILCMASHDKGETWGTKIVIKYDNYKLGVQYFFLRPYISKNDLSFHFYVGDNINNVKNVNFIECTHEKDLEFVCSNRDFLKDNKVLQDVSTLNDEYIVSYGNDNNFAECYIFFNNENSILIKPEKYGNTAAGCYGGTFVKIDENRALFIYSSSQGIYNIHTIYYANYEGGGGSEPEA |
Interaction
1、Solvent accessible surface areas (SASA) were calculated (Naccess V2.1.1) for each residue in antibody and antigen, respectively. The residues with SASA loss in binding of more than 1Å2 were classified as interacting residues.
Interacting residues (ΔSASA based)
| D: SER46 SER47 SER48 TYR49 ASN69 GLN70 LYS71 LYS84 ARG109 ASN111 E: SER50 SER51 THR53 SER72 SER73 GLY74 GLY76 ASN78 ASN121 GLY122 CYS123 ASP124 TRP125 SER126 TYR127 B: GLU112 GLU113 ARG135 TYR137 ASN139 ASP140 GLU143 ASN145 ASN146 ALA147 GLU148 ILE149 ARG174 HIS202 ASP203 LYS204 GLU206 THR207 GLY209 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 5Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 5 Å from any atom.
Interacting residues (Atom distance based)
