Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5966 |
| PDBID: | 8DEF |
| Chains: | ST_G |
| Organism: | Western equine encephalitis virus, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 4.20 |
| Reference: | 10.1016/j.cell.2023.05.019 |
| Antibody | |
| Antibody: | SKW24 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Venezuelan equine encephalitis virus-like particle (VLP) spike glycoprotein E2 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: S
Mutation: NULL
| >8DEF_S|Chain G[auth S], I[auth U]|SKW24 Fab heavy chain|Homo sapiens (9606) EVQLVESGGGLVQPGGSLRLSCVASGFTFSDYRMAWVRQATGKGLEWVSTISQPSGTNTYYLDPVKGRFTVSRDNAKNTLYLQMHSLRAEDTAVYYCARVVTESRPPAAWFDVWGPGVLVTVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCGGLEVLFQ |
Light Chain: T
Mutation: NULL
| >8DEF_T|Chain H[auth T], J[auth V]|SKW24 Fab light chain|Homo sapiens (9606) SYELTQPPSVSASPGQTARITCGGINIGSELVHWYQQKPPQAPVLVIYANGERPSGIPERFSGSNSGNTATLTISGVEAGDEADYYCQLWDISSDHNYIFGDGTRLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVEVAWKADGSAVNAGVETTKPSKQSNNKYAASSYLSLTSDQWKSHKSYSCQVTHEGSTVEKTVAPAECS |
Antigen
Chain: G
Mutation: NULL
| >8DEF_G|Chain B, D[auth G], F[auth K]|Spike glycoprotein E2|Western equine encephalitis virus (11039) SITDDFTLTSPYLGFCPYCRHSAPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTADVTKFRYMSFDHDHDIKEDSMDKIAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGASENSCTVEKKIRRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYLEEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKSDQTKWVFNSPDLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTATRPTLLTTRKLGLRADATAEWITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYYHRHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVPTALAVLCCI |
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)
| S: ARG33 SER52 GLN53 PRO54 THR57 ASN58 TYR60 THR102 GLU103 SER104 ARG105 PRO106 PRO107 T: GLY28 SER29 LEU31 ALA49 ASN50 GLY51 ASN65 TRP90 ILE92 SER93 HIS96 G: ARG173 PRO176 ALA178 THR201 TYR202 GLU203 LYS205 GLY207 ASP208 TYR209 SER210 THR211 GLY212 ILE213 ASN221 ILE230 TYR232 SER234 GLN236 ILE247 ARG248 HIS249 THR250 ASP251 SER253 GLN255 |
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)
