Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1538 |
| PDBID: | 5KZC |
| Chains: | BD_C |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.25 |
| Reference: | 10.1371/journal.ppat.1005815 |
| Antibody | |
| Antibody: | VRC01 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | HIV-1 gp120 engineered outer domain |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: B
Mutation: NULL
| >5KZC_B|Chain A[auth B], D[auth E], G[auth H]|VRC01 Fab heavy chain|Homo sapiens (9606) QVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRGGAVNYARPLQGRVTMTRDVYSDTAFLELRSLTVDDTAVYFCTRGKNCDYNWDFEHWGRGTPVIVSSPSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: D
Mutation: NULL
| >5KZC_D|Chain C[auth D], F[auth G], I[auth L]|VRC01 Fab light chain|Homo sapiens (9606) EIVLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRFSGSRWGPDYNLTISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC |
Antigen
Chain: C
Mutation: NULL
| >5KZC_C|Chain B[auth A], E[auth C], H[auth F]|Engineered outer domain of gp120|Homo sapiens (9606) DTITLPCRPAPPPHCSSNITGLILTRDGGNSNAESEIFRPGGGDMRDIARCQIAGTVVSSQLFLNGSLAEEEVVIRSVNFTDNAKSICVQLATSVEIACTGAGHCAISRAKWANTLKQIASKLREQFGNAKTIIFKQSSGGDPEIVTHWFNCGGEFFYCASTQLFASTWFASTGTKHHHHHH |
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 ASP31 THR33 TRP47 TRP50 PRO52 ARG53 GLY54 GLY55 ALA56 VAL57 ASN58 TYR59 ALA60 ARG61 PRO62 GLN64 ARG71 CYS98 ASP99 D: ILE2 VAL3 GLN27 TYR28 TYR91 GLU96 PHE97 C: THR25 ARG26 ASP27 GLY28 GLY29 ASN30 ALA33 SER35 GLU36 ILE37 ARG39 GLY42 GLY43 ASP44 MET45 ARG46 ASP47 ILE48 ARG50 VAL78 ASN79 THR81 ASP82 ASN83 ALA84 LYS85 SER86 SER139 GLY140 GLY141 ASP142 GLU144 ILE145 |
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)
