Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2912 |
| PDBID: | 6UDK |
| Chains: | DE_G |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.90 |
| Reference: | 10.1016/j.cell.2020.01.010 |
| Antibody | |
| Antibody: | 1-55 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 BG505 SOSIP gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: D
Mutation: NULL
| >6UDK_D|Chain J[auth D], L[auth H], N[auth M]|1-55 Fab Heavy Chain|Homo sapiens (9606) MGWSCIILFLVATATGAHSQGRLFQSGTEVKRPGASVKISCRADDDPYTDDDTFTKYYTHWIRQAPGQPPEWLGVISPHFARPIYSYKFRDRLTLTRDSSLTAVYFELRGLQPDDTGIYFCARDPFGDMYPHYNYHMDVWGGGTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH |
Light Chain: E
Mutation: NULL
| >6UDK_E|Chain K[auth E], M[auth L], O[auth N]|1-55 Fab Light Chain|Homo sapiens (9606) MGWSCIILFLVATATGVHSEIVLTQSPAILSVSPGDRVILSCKASEGLSSSDLAWYRFKGGQIPTLVIFGASNRARGTPDRFSGSGSGTDFTLTINRVEPEDFATYYCQRYGGTPITFGGGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: G
Mutation: NULL
| >6UDK_G|Chain A[auth G], B[auth K], C[auth R]|RC1 variant of HIV-1 Env glycoprotein gp120|Human immunodeficiency virus 1 (11676) AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNYAPNLLSNMRGELKQCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNTPVQINCTRPNNNTVKSIRIGPGQAFYYFGDIIGDIRMAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSIVLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR |
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)
| D: PRO28 TYR29 THR30 ASP31 ASP32 ASP33 PRO52 HIS53 PHE54 ALA55 ARG56 PRO57 ILE58 TYR59 SER60 TYR61 ARG64 THR70 ARG71 ASP72 SER73 SER74 LEU75 PHE97 GLY98 ASP99 E: GLU1 GLY92 GLY93 THR94 PRO95 G: GLU49 TRP96 LYS97 ASN99 GLU102 ILE194 ASN195 ASN197 THR198 THR257 THR278 ASN279 ASN280 ALA281 LYS282 ASN283 SER364 SER365 GLY366 GLY367 ASP368 GLU370 VAL371 ASN425 MET426 TRP427 GLN428 ARG429 ILE430 THR455 ARG456 ASP457 GLY458 GLY459 SER460 THR461 ARG469 GLY471 GLY472 GLY473 ASP474 MET475 ARG476 ARG480 |
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)
