Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3945 |
| PDBID: | 7KHF |
| Chains: | HB_C |
| Organism: | Homo sapiens, Plasmodium falciparum 3D7 |
| Method: | EM |
| Resolution (Å): | 3.54 |
| Reference: | 10.1038/s41586-021-03378-6 |
| Antibody | |
| Antibody: | MDB1 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Plasmodium RIFIN (PF3D7_1373400) V2 domain |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7KHF_H|Chain A, C[auth H]|MDB1 Fab heavy chain|Homo sapiens (9606) QITLKESGPTLVERTQTLTLTCTFSGFSLTTDGLGVGWIRQPPGKALEWLALIYYDDVRRYRPSLKSRLTITKDTSKNRVVLTVTDMDPVDAGTYFCVHASLFNLGSRNVYFRYWGQGTLVSVSSGVSKKPSLSVQPGPIVAPEETLTLQCGSDAGYNRFVLYKDGERDFLQLAGAQPQAGLSQANFTLGPVSRSYGGQYRCYGAHNLSSEWSAPSDPLDILIAGQFYDRVSLSVQPGPTVASGENVTLLCQSQGWMQTFLLTKEGAADDPWRLRSTYQSQKYQAEFPMGPVTSAHAGTYRCYGSQSSKPYLLTHPSDPLELVVSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKY |
Light Chain: B
Mutation: NULL
| >7KHF_B|Chain B, D[auth L]|MDB1 Fab light chain|Homo sapiens (9606) SYDLTQPPSVSVSPGQTARITCSGDSLARQFASWYQQKPGQSPVLLIYKNIERLSAIPERFSGSTSGTSVTLTISGVQAEDEADYFCQSADDSGSYSLFGTGTRVSVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS |
Antigen
Chain: C
Mutation: NULL
| >7KHF_C|Chain E[auth C], F[auth D]|Rifin|Plasmodium falciparum (isolate 3D7) (36329) KELAEKAGALAGEAARIPAAIDAVIEGIKSKFSIDTLGGEALKSVIDGTNYYDASYITTAIYNKFQVSSCLPSVPFLGGPPVPGAGANKPICSAVDKLYLGSGNFLDKSSLPGSIQKDVAKIVAGAEQAAKAKAAMVASDKTLAVETAKKQ |
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)
| Chain residues position delta_SASA
: residuesposition H: ARG159 VAL161 TYR163 ASP165 GLY166 GLU167 ARG168 ASP169 PHE170 LEU171 GLN172 LEU173 ALA174 GLY175 ALA176 GLN177 ASN186 PHE187 THR188 TYR203 ASN207 LEU208 SER209 SER210 GLU211 TRP212 SER213 PRO215 C: CYS242 LEU243 PRO244 SER245 VAL246 PRO247 PHE248 LEU249 GLY250 GLY251 PRO252 PRO253 VAL254 PRO255 ALA259 ASN260 ASP268 LYS269 LEU272 GLY273 SER274 GLY275 ASN276 PHE277 LEU278 ASP279 LYS280 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
