Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1111 |
| PDBID: | 4YDL |
| Chains: | BC_A |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 1.80 |
| Reference: | 10.1016/j.cell.2015.05.007 |
| Antibody | |
| Antibody: | C38-VRC18.02 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 clade AE strain 93TH057 gp120 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: B
Mutation: NULL
| >4YDL_B|Chain B, E[auth H]|HEAVY CHAIN OF ANTIBODY C38-VRC18.02|Homo sapiens (9606) QVRLVQSGNQVRKPGASVRISCEASGYKFIDHFIHWVRQVPGHGLEWLGWINPRGGGVNYSRSFQGKLSMTMTRDNFEETAYLDLSKLNPGDTAVYFCARGFAGYEWSFIWGQGTLVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK |
Light Chain: C
Mutation: NULL
| >4YDL_C|Chain C, F[auth L]|LIGHT CHAIN OF ANTIBODY C38-VRC18.02|Homo sapiens (9606) EIVLTQSPGTLSLSPGETATLSCRTSQGILSNQLAWHQQRRGQPPRLLIYGGSNRAPGIPERFTGSGSGTDFVLTIKRLERDDFAVYYCQILEFFGRGTRVEMNRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: NULL
| >4YDL_A|Chain A, D[auth G]|Envelope glycoprotein gp160,Envelope glycoprotein gp160|Human immunodeficiency virus 1 (11676) VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE |
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)
| B: ILE30 PHE33 TRP47 TRP50 ARG53 GLY54 GLY55 GLY56 VAL57 ASN58 TYR59 SER60 ARG61 SER62 GLN64 ARG73 ASN75 PHE76 C: GLU1 ILE2 LEU29 GLN32 LEU91 GLU96 PHE97 A: GLN105 THR123 GLY124 ASN276 THR278 ASN279 ASN280 ALA281 LYS282 SER365 GLY366 GLY367 ASP368 ILE371 TRP427 GLN428 GLY429 THR430 THR455 ARG456 ASP457 GLY458 GLY459 ALA460 ASN461 ASN462 THR463 ASN465 GLU466 THR467 ARG469 GLY472 GLY473 ASN474 |
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)
