Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6104 |
| PDBID: | 8E99 |
| Chains: | E_B |
| Organism: | Homo sapiens, Lama glama |
| Method: | EM |
| Resolution (Å): | 4.24 |
| Reference: | 10.1016/j.molcel.2022.10.008 |
| Antibody | |
| Antibody: | 4 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Glutamate receptor ionotropic, NMDA 2A |
| Antigen mutation: | No |
| Durg Target: | Q12879 |
Sequence information
Antibody
Chain: E
Mutation: NULL
| >8E99_E|Chain E|Nanobody 4|Lama glama (9844) MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQAGGSLRLSCAASAAAAAAAAAGWYRQAPGKERAAAAAAAAAAAAAAADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAAAAAAAAAAYWGQGTQVTVSSGSGSSRLEEELRRRLTEHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >8E99_B|Chain B|Glutamate receptor ionotropic, NMDA 2A|Homo sapiens (9606) GSGATNFSLLKQAGDVEENPGPMGTMRLFLLAVLFLFSFARATGGPPALNIAVMLGHSHDVTERELRTLWGPEQAAGLPLDVNVVALLMNRTDPKSLITHVCDLMSGARIHGLVFGDDTDQEAVAQMLDFISSHTFVPILGIHGGASMIMADKDPTSTFFQFGASIQQQATVMLKIMQDYDWHVFSLVTTIFPGYREFISFVKTTVDNSFVGWDMQNVITLDTSFEDAKTQVQLKKIHSSVILLYSSKDEAVLILSEARSLGLTGYDFFWIVPSLVSGNTELIPKEFPSGLISVSYDDWDYSLEARVRDGIGILTTAASSMLEKFSYIPEAKASCYGQMERPEVPMHTLHPFMVNVTWDGKDLSFTEEGYQVHPRLVVIVLNKDREWEKVGKWENHTLSLRHAVWPRYKSFSDSEPDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFSIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRSNGTVSPSAFLEPFSASVWVMMFVMLLIVSAIAVFVFEYFSPVGYNRNLAKGKAPHGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEFVDQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTKFNQKGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICHNEKNEVMSSQLDIDNMAGVFYMLAAAMALSLITFIWEHLFYWKLRFSFTGTETSQVAPA |
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 E: ALA27 ALA28 ALA30 ALA31 ALA33 ALA46 ALA47 ALA50 ALA51 ALA52 ALA54 ALA56 ALA58 ALA60 ASN73 ALA98 ALA99 ALA100 ALA101 ALA102 ALA103 ALA104 ALA105 B: ASN367 LYS368 GLU373 ARG386 HIS387 ALA388 VAL389 TRP390 PRO391 ARG392 TYR393 LYS394 ASP402 ASP403 PHE439 GLU448 GLY449 MET450 ASN451 VAL492 VAL501 TYR502 GLN503 ARG504 VAL506 |
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)
