Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2680 |
| PDBID: | 6P65 |
| Chains: | FG_E |
| Organism: | Human immunodeficiency virus 1, Oryctolagus cuniculus |
| Method: | EM |
| Resolution (Å): | 3.94 |
| Reference: | 10.1016/j.immuni.2019.10.008 |
| Antibody | |
| Antibody: | 1C2 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 clone 16055 gp160 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: F
Mutation: NULL
| >6P65_F|Chain B[auth C], E[auth F], H|Rabbit antibody 1C2 heavy chain fragment antigen binding|Oryctolagus cuniculus (9986) MYRMQLLSCIALSLALVTNSQCQSLEESGGDLVKPGASLTLTCTASGFSFGWNDYMSWVRQAPGKGLEWIGCIYAGSTRSTYYANWAKGRLTISKTSSTAVTLQMTSLTAADTATYFCARGAVTYDGLGGAYLKHFNLWGPGTLVTVSSGQPKAPSVFPLAPCCGDTPSSTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVTSSSQPVTCNVAHPATNTKVDKTVAPSTCSKHHHHHHHH |
Light Chain: G
Mutation: NULL
| >6P65_G|Chain C[auth D], F[auth G], I[auth L]|Rabbit antibody 1C2 kappa chain|Oryctolagus cuniculus (9986) MYRMQLLSCIALSLALVTNSAIKMTQTPSSVSAAVGGTVTVNCRASEDIESYLAWYQQKPGQPPKLLIYDTSKLASGVPSRFKGSGSGTQFALTISGVQCDDAATYYCLYGYISSDRIDFGFGGGTELVVKGDPVAPSVLIFPPAADQVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSSTLTLTSTQYNSHKEYTCKVTQGTTSVVQSFNRGDC |
Antigen
Chain: E
Mutation: NULL
| >6P65_E|Chain A, D[auth B], G[auth E]|HIV Env 16055 NFL TD 2CC+|Human immunodeficiency virus 1 (11676) MPMGSLQPLATLYLLGMLVASVLANGNLWVTVYYGVPVWKDAETTLFCASDAKAYEKEKHNVWATHACVPTDPNPQEMVLENVTENFNMWKNDMVEQMHTDVISLWDQSLKPCVKLTPLCVTLECRQVNTTNATSSVNVTNGEEIKNCSFNATTELRDKKQKVYALFYRLDIVPLEEERKGNSSKYRLINCNTSACTQACPKVTFDPIPIHYCAPAGYAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEGEIIIRSENLTNNVKTIIVHLNESVEIVCTRPNNYTRKSIRIGPGQTFYATGDIIGNIRQAYCNISKDDWIRTLQRVGKKLAEHFPRRIINFTSPAGGDLEITTHSFNCRGEFFYCNTSSLFNSTYNPNDTNSNSSSSNSSLDITIPCRIKQIINMWQRVGQCMYAPPIEGNITCKSNITGLLLVRDGGVESNETEIFRPGGGDMRNNWRSELYKYKVVEIKPLGIAPTRCKRRVVEGGGGSGGGGSDDDDKAVGLGAVRRGFLGAAGSTMGAASITLTVQARQLLSGIVQQQSNLLKAPEAQQHLLQLGVWGIKQLQTRVLAIERYLKDQQLLGIWGCSGKLICTTAVPWNSSWSNKSHDEIWGNMTWMQWDREIGNYTNTIYRLLEDSQNQQEQNEKDLLACDGGGGSHHHHHHHH |
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)
| F: TRP31 ASN32 GLY52 SER53 THR54 ARG55 LYS71 THR98 TYR99 G: GLU30 TYR32 ILE93 SER94 E: THR37 TYR39 GLU87 ASN88 THR499 ARG500 CYS501 GLY524 ALA525 ALA526 GLY527 SER528 THR529 GLY531 ALA532 SER534 ILE535 THR536 THR538 VAL539 ILE603 THR605 HIS619 ASP620 TRP623 GLY624 ASN625 THR627 GLN630 |
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)
