Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3955 |
| PDBID: | 7KJI |
| Chains: | A_B |
| Organism: | Vicugna pacos, Plasmodium falciparum 3D7 |
| Method: | XRD |
| Resolution (Å): | 3.25 |
| Reference: | 10.1042/BCJ20200415 |
| Antibody | |
| Antibody: | D9 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Plasmodium falciparum protein Pf12p |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: A
Mutation: NULL
| >7KJI_A|Chain A|Nanobody D9|Vicugna pacos (30538) QVQLQESGGGLVQPGGSLRLSCAASGIIFSSHVMGWYRQAPGKQRELVASFSGDTGAKYADSVKGRFIIRRENAKNMVTLYLQMNSLKPEDTAAYYCHVDRFGTEYWGQGTQVTVSSHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >7KJI_B|Chain B|Surface protein P12p|Plasmodium falciparum (36329) GASNGVCDFSSEGLSLLPEEKLDFSVSRNVDKLSDENNVRHCVHFSKGFEYLRFICPMRKDNYEGIEIRPVECFEYIHIEGREHKLSEILKGSLYEKSINDNIMTRDVFIPPTIYEDMFFECTCDNSLTFKNNMIGIRGIMKIHLKKNILYGCDFDHDEKLMKNKTAFTNFYDKQKILPLIGNNNNDDDNNDDDNNNDNNNNDNNNNNNNNNNNNNNNNNNNITCNVTIKKSQVYLGIICPDGYTLYPNDCFKNVIYDNNIIIPLKKIIPHDILYHQDKNKRITFASFTLNINENPPGFTCYCIKDQTNINNPLIVNFHFS |
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 A: GLN1 SER25 GLY26 ILE27 ILE28 PHE29 SER30 SER31 HIS32 ASN73 ALA74 LYS75 ASN76 VAL78 ASP100 ARG101 PHE102 GLY103 THR104 GLU105 TYR106 B: SER23 GLY25 VAL26 ASP28 TYR71 LEU72 ARG73 ILE75 LEU114 TYR115 GLU116 ASN120 ILE123 THR125 ASP127 VAL128 LYS273 ILE293 LEU294 TYR295 HIS296 GLN297 ASP298 LYS299 |
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)
