Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6123 |
| PDBID: | 8EEV |
| Chains: | ST_F |
| Organism: | Venezuelan equine encephalitis virus, Macaca fascicularis |
| Method: | EM |
| Resolution (Å): | 3.60 |
| Reference: | 10.1016/j.cell.2023.05.019 |
| Antibody | |
| Antibody: | SKT20 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Venezuelan equine encephalitis virus-like coat protein |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: S
Mutation: NULL
| >8EEV_S|Chain E[auth H], I[auth S], K[auth U]|Fab SKT20 heavy chain|Macaca fascicularis (9541) QVQVQESGPGLVKPSETLSLTCAVSSGSINDDSYYWTWIRQSPGKGLEWLGFIHGGTGKSFYNPSLESRVTISKDTSRNQFSLTLSSVSAADTAVYYCARSHFCSNTFCYGWFDVWGPGIRVTVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCGGLEVLFQ |
Light Chain: T
Mutation: NULL
| >8EEV_T|Chain H[auth L], J[auth T], L[auth V]|Fab SKT20 light chain|Macaca fascicularis (9541) DVVMTQTPLSLPITPGEPASISCRSSQSLLHSNGNTYLHWYLQKPGQSPQLLIYGGSNRASGVPDRFSGSGSGTDFTLKISKVEAEDVGVYYCVQAIAFPWTFGQGTKVEIKRTVAAPSVFIFPPSEDQVKSGTVSVVCLLNNFYPREASVKWKVDGALKTGNSQESVTEQDSKDNTYSLSSTLTLSSTEYQSHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: F
Mutation: NULL
| >8EEV_F|Chain A, B, C[auth F], D[auth G], F[auth J], G[auth K]|Coat protein|Venezuelan equine encephalitis virus (11036) MFPFQPMYPMQPMPYRNPFAAPRRPWFPRTDPFLAMQVQELTRSMANLTFKQRRDAPPEGPSAKKPKKEASQKQKGGGQGKKKKNQGKKKAKTGPPNPKAQNGNKKKTNKKPGKRQRMVMKLESDKTFPIMLEGKINGYACVVGGKLFRPMHVEGKIDNDVLAALKTKKASKYDLEYADVPQNMRADTFKYTHEKPQGYYSWHHGAVQYENGRFTVPKGVGAKGDSGRPILDNQGRVVAIVLGGVNEGSRTALSVVMWNEKGVTVKYTPENCEQWSLVTTMCLLANVTFPCAQPPICYDRKPAETLAMLSVNVDNPGYDELLEAAVKCPGRKRRSTEELFNEYKLTRPYMARCIRCAVGSCHSPIAIEAVKSDGHDGYVRLQTSSQYGLDSSGNLKGRTMRYDMHGTIKEIPLHQVSLYTSRPCHIVDGHGYFLLARCPAGDSITMEFKKDSVRHSCSVPYEVKFNPVGRELYTHPPEHGVEQACQVYAHDAQNRGAYVEMHLPGSEVDSSLVSLSGSSVTVTPPDGTSALVECECGGTKISETINKTKQFSQCTKKEQCRAYRLQNDKWVYNSDKLPKAAGATLKGKLHVPFLLADGKCTVPLAPEPMITFGFRSVSLKLHPKNPTYLITRQLADEPHYTHELISEPAVRNFTVTEKGWEFVWGNHPPKRFWAQETAPGNPHGLPHEVITHYYHRYPMSTILGLSICAAIATVSVAASTWLFCRSRVACLTPYRLTPNARIPFCLAVLCCARTARAETTWESLDHLWNNNQQMFWIQLLIPLAALIVVTRLLRCVCCVVPFLVMAGAAAPAYEHATTMPSQAGISYNTIVNRAGYAPLPISITPTKIKLIPTVNLEYVTCHYKTGMDSPAIKCCGSQECTPTYRPDEQCKVFTGVYPFMWGGAYCFCDTENTQVSKAYVMKSDDCLADHAEAYKAHTASVQAFLNITVGEHSIVTTVYVNGETPVNFNGVKITAGPLSTAWTPFDRKIVQYAGEIYNYDFPEYGAGQPGAFGDIQSRTVSSSDLYANTNLVLQRPKAGAIHVPYTQAPSGFEQWKKDKAPSLKFTAPFGCEIYTNPIRAENCAVGSIPLAFDIPDALFTRVSETPTLSAAECTLNECVYSSDFGGIATVKYSASKSGKCAVHVPSGTATLKEAAVELTEQGSATIHFSTANIHPEFRLQICTSYVTCKGDCHPPKDHIVTHPQYHAQTFTAAVSKTAWTWLTSLLGGSAVIIIIGLVLATIVAMYVLTNQKHN |
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 S: SER33 PHE50 THR54 LYS56 PHE58 CYS98 SER99 T: SER27 ASN28 TYR32 ALA91 ILE92 PHE94 TRP96 F: CYS63 PHE87 MET88 TRP89 GLY91 TYR93 PHE95 CYS96 ASP97 GLU99 GLY227 |
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)
