Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 225 |
| PDBID: | 2CMR |
| Chains: | HL_A |
| Organism: | Human immunodeficiency virus 1, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.00 |
| Reference: | 10.1038/nsmb1127 |
| Antibody | |
| Antibody: | D5 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 gp41 inner-core mimetic 5-helix |
| Antigen mutation: | No |
| Durg Target: | Q53I07; P35961; |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >2CMR_H|Chain B[auth H]|D5|HOMO SAPIENS (9606) QVQLVQSGAEVRKPGASVKVSCKASGDTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANYAQAFQGRVTITANESTSTAYMELSSLRSEDTAIYYCARDNPTLLGSDYWGAGTLVTVSSASTKGPSVFPLAPCSRSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRV |
Light Chain: L
Mutation: NULL
| >2CMR_L|Chain C[auth L]|D5|HOMO SAPIENS (9606) DIQMTQSPSTLSASIGDRVTITCRASEGIYHWLAWYQQKPGKAPKLLIYKASSLASGAPSRFSGSGSGTDFTLTISSLQPDDFATYYCQQYSNYPLTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKS |
Antigen
Chain: A
Mutation: NULL
| >2CMR_A|Chain A|TRANSMEMBRANE GLYCOPROTEIN|HUMAN IMMUNODEFICIENCY VIRUS 1 (11676) MQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAGGSGGHTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLEGSSGGQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAGGSGGHTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLEGSSGGQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAGGHHHHHHG |
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: SER30 SER31 TYR32 ALA33 GLY50 ILE51 ILE53 PHE54 GLY55 THR56 ALA57 ASN58 TYR59 GLU73 ASP95 ASN96 PRO97 THR98 L: TYR30 HIS31 TRP32 LYS50 TYR91 SER92 ASN93 TYR94 A: VAL29 ILE32 LYS33 GLN36 LEU40 ASP142 ARG143 ASN146 ASN147 THR149 SER150 HIS153 GLU195 HIS199 LEU200 GLN202 LEU203 THR204 TRP206 GLY207 LYS209 GLN210 LEU211 ALA213 ARG214 |
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)
