Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6892 |
| PDBID: | 4JPK |
| Chains: | HL_A |
| Organism: | Homo sapiens, Human immunodeficiency virus 1 |
| Method: | XRD |
| Resolution (Å): | 2.40 |
| Reference: | 10.1126/science.1234150 |
| Antibody | |
| Antibody: | GL-VRC01 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 gp120 engineered outer domain eOD-GT6 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >4JPK_H|Chain A[auth H]|Putative VRC01 germline precursor Fab heavy chain|Homo sapiens (9606) QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARGKNSDYNWDFQHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTKLGGSGGHHHHHHGGSGHG |
Light Chain: L
Mutation: NULL
| >4JPK_L|Chain B[auth L]|Putative VRC01 germline precursor Fab light chain|Homo sapiens (9606) EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQYEFFGQGTKLEIKRSTVAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: A
Mutation: NULL
| >4JPK_A|Chain C[auth A]|Germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6|Human immunodeficiency virus 1 (11676) DTITLPCRPAPPPHCSSNITGLILTRDGGVSNDETEIFRPSGGDMRDIARCQIAGTVVSTQLFLNGSLAEEEVVIRSVDFRDNAKSICVQLATSVEIACTGAGHCAISRAKWANTLKQIASKLREQFGARTIIFKQSSGGDPEFVTHSFNCGGEFFYCDSTQLFASTWFAST |
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)
| H: THR30 GLY31 TYR33 TRP47 TRP50 ASN53 SER54 GLY55 GLY56 THR57 ASN58 TYR59 ALA60 GLN61 LYS62 GLN64 ARG71 SER98 ASP99 L: GLU1 ILE2 GLN27 SER28 VAL29 TYR32 TYR91 GLU96 PHE97 A: THR25 ARG26 ASP27 GLY28 GLY29 VAL30 SER31 ASN32 GLU36 ILE37 ARG39 GLY42 GLY43 ASP44 ARG46 ASP47 VAL78 ASP79 ARG81 ASP82 ASN83 ALA84 LYS85 SER138 GLY139 GLY140 ASP141 PHE144 |
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)
