Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 645 |
| PDBID: | 3RU8 |
| Chains: | HL_X |
| Organism: | Human immunodeficiency virus, synthetic construct, Thermobifida fusca, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.07 |
| Reference: | 10.1126/science.1209368 |
| Antibody | |
| Antibody: | b12 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 Epitope Scaffold 2bodx43 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >3RU8_H|Chain B[auth H]|Antibody b12, Heavy Chain|Homo sapiens (9606) QVQLVQSGAEVKKPGASVKVSCQASGYRFSNFVIHWVRQAPGQRFEWMGWINPYNGNKEFSAKFQDRVTFTADTSANTAYMELRSLRSADTAVYYCARVGPYSWDDSPQDNYYMDVWGKGTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: L
Mutation: NULL
| >3RU8_L|Chain C[auth L]|Antibody b12, Light Chain|Homo sapiens (9606) EIVLTQSPGTLSLSPGERATFSCRSSHSIRSRRVAWYQHKPGQAPRLVIHGVSNRASGISDRFSGSGSGTDFTLTITRVEPEDFALYYCQVYGASSYTFGQGTKLERKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC |
Antigen
Chain: X
Mutation: NULL
| >3RU8_X|Chain A[auth X]|Epitope Scaffold 2bodx43|Human immunodeficiency virus (12721) DSPFYVNPNMSSAEWVRNNPNDPRTPVIRNRIASVPQGTWHNQHNPGQITGQVDALMSAAQAAGKIPILVVDVGPTGDMSQGEEAGKQWIDEFAAGLKNRPAYIIVYPLYSGGDPEIVQEWLRTVAYAGKALKAGSSQARIYFDAGHSAWHSPAQMAAALQRADISNSAHGIATNTSNYRWTADEVAYAKAVLSAIGNPSLRAVIDTSRNGNGPAGNESCDPSGRAIGTPSTTNTGDPMIDAFLWIKLPGEADGCIAGAGQFVPQAAYEMAIAALEHHHHHH |
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: GLN1 GLN3 GLY26 ARG28 SER30 ASN31 PHE32 VAL33 PRO52 TYR53 ASN54 THR73 VAL95 PRO97 TYR98 SER99 L: ARG46 ARG55 ALA56 SER57 GLY58 ILE59 X: ASP72 GLY74 PRO75 THR76 GLY77 ASP78 MET79 PRO108 TYR110 SER111 GLY112 GLY113 ASP114 PRO115 GLU116 ILE117 VAL118 GLN119 GLU120 TRP121 LEU122 TRP150 HIS151 GLN155 ALA158 ALA159 ARG162 ASN217 GLU218 SER219 CYS220 ASP253 GLY254 CYS255 ALA259 |
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)
