Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5969 |
| PDBID: | 8DER |
| Chains: | XY_B |
| Organism: | Macaca, Venezuelan equine encephalitis virus |
| Method: | EM |
| Resolution (Å): | 3.30 |
| Reference: | 10.1016/j.cell.2023.05.019 |
| Antibody | |
| Antibody: | SKV16 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: X
Mutation: NULL
| >8DER_X|Chain A[auth H], I[auth W], K[auth X]|SKV16 Fab Heavy Chain|Macaca (9539) VQLVESGGGLAKPGGSLRLSCAAAGFRFSDFHMHWVRQAPGKGLEWVSRISHGGVTTRFADSVKGRFTISRENAKNTLYLQMDNLRAEDTAVYYCARDSPYWGDYSHSLDVWGRGVLVTVSS |
Light Chain: Y
Mutation: NULL
| >8DER_Y|Chain B[auth L], J[auth V], L[auth Y]|SKV16 Fab Light Chain|Macaca (9539) PMRLTQPRSVSVSPGQTARITCGGDNIGSKSVHWYQQKPPQAPVLVIYDDRARPSGIPERFSGSKSGNTATLAISGVEAGDEADYYCQVWDSSSDVLFGGGTRLT |
Antigen
Chain: B
Mutation: NULL
| >8DER_B|Chain E[auth A], G[auth B], H[auth C]|Spike glycoprotein E2|Venezuelan equine encephalitis virus (11036) STEELFNEYKLTRPYMARCIRCAVGSCHSPIAIEAVKSDGHDGYVRLQTSSQYGLDSSGNLKGRTMRYDMHGTIKEIPLHQVSLYTSRPCHIVDGHGYFLLARCPAGDSITMEFKKDSVRHSCSVPYEVKFNPVGRELYTHPPEHGVEQACQVYAHDAQNRGAYVEMHLPGSEVDSSLVSLSGSSVTVTPPDGTSALVECECGGTKISETINKTKQFSQCTKKEQCRAYRLQNDKWVYNSDKLPKAAGATLKGKLHVPFLLADGKCTVPLAPEPMITFGFRSVSLKLHPKNPTYLITRQLADEPHYTHELISEPAVRNFTVTEKGWEFVWGNHPPKRFWAQETAP |
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)
| X: ARG28 ASP31 PHE32 HIS33 HIS52 GLY53 VAL55 THR56 ASP95 PRO97 TYR98 TRP99 B: SER180 LEU181 SER182 THR187 THR189 PRO190 ASP192 GLY193 GLU209 THR210 ILE211 ASN212 LYS213 THR214 LYS215 GLN216 SER218 |
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)
