Details
Structure visualisation
Key: Loading Structure... |
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Entry information
| Complex | |
| AACDB_ID: | 6121 |
| PDBID: | 8EEU |
| Chains: | HL_A |
| Organism: | Venezuelan equine encephalitis virus, Macaca fascicularis |
| Method: | EM |
| Resolution (Å): | 3.50 |
| Reference: | 10.1016/j.cell.2023.05.019 |
| Antibody | |
| Antibody: | SKT05 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: H
Mutation: NULL
| >8EEU_H|Chain G[auth H]|Fab SKT05 heavy chain|Macaca fascicularis (9541) EVQLVESGAGLVQPGGSLRLSCAASGFTFSDSWMSWVRQSPGKGLEWVGRIKGKPDGETAAYAASVKGRFSISRDDSKNTLYLQMNSLKTEDTAVYYCTRDDRTSCRRGVCYAAFHSWGQGVLVTVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCGGLEVLFQ |
Light Chain: L
Mutation: NULL
| >8EEU_L|Chain H[auth L]|Fab SKT05 light chain|Macaca fascicularis (9541) DIQMTQSPSSLSASAGDRVTLTCRASQAISFYLAWYQQKPGKAPKRLIYDASELQGGVPSRFSGSGSGTDFTLSINSLQPEDSATYFCLQYDSPPFTFGPGTKVEIKRTVAAPSVFIFPPSEDQVKSGTVSVVCLLNNFYPREASVKWKVDGALKTGNSQESVTEQDSKDNTYSLSSTLTLSSTEYQSHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: NULL
| >8EEU_A|Chain A, B, C, D, E, F|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 H: ASP31 SER32 TRP33 PRO52 ASP53 ARG94 ASP95 ASP96 ARG97 THR98 SER99 HIS101 L: PHE31 ARG46 TYR49 ASP50 SER52 GLU53 LEU54 GLN55 GLY56 GLY57 VAL58 SER60 A: GLY64 SER65 GLN66 GLU67 CYS68 THR69 PRO70 TYR72 ASP75 GLU76 GLN77 CYS78 LYS79 VAL80 PHE81 THR82 THR98 GLU99 TYR214 ALA215 ASN216 ASN218 VAL220 ARG223 |
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)
