Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 2848 |
| PDBID: | 6SVL |
| Chains: | DE_F |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 1.58 |
| Reference: | 10.1038/s41467-019-13343-7 |
| Antibody | |
| Antibody: | Ab8 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Myeloid-derived growth factor (MYDGF) |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: D
Mutation: NULL
| >6SVL_D|Chain A, D, G, H, K, O|Fab_heavy_chain|Homo sapiens (9606) EVQLQQSGAELVRPGALVKLSCKASGFNIKDYYMHWVKQRPEQGLEWIGRIDPENSNNIYDPKFQGKASITADTSSNTAYLQLSSLTSEDTAVYYCARGGFDTNHYAMDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHEQKLISEEDLHHHHHH |
Light Chain: E
Mutation: NULL
| >6SVL_E|Chain B, E, I, L, M, P|Fab_light_chain|Homo sapiens (9606) MGWSLILLFLVAVATRVLSDIQMTQSPASLSVSVGETVTITCRASENIYSNLAWYQQKQGKSPQLLVYAATNLADGVPSRFSGSGSGTQYSLKINSLQSEDFGNYYCQHFWGTPPWTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: F
Mutation: NULL
| >6SVL_F|Chain C, F, J, N, Q, R|Myeloid-derived growth factor|Homo sapiens (9606) VSEPTTVAFDVRPGGVVHSFSHNVGPGDKYTCMFTYASQGGTNEQWQMSLGTSEDHQHFTCTIWRPQGKSYLYFTQFKAEVRGAEIEYAMAYSKAAFERESDVPLKTEEFEVTKTAVAHRPGAFKAELSKLVIVAKASRTEL |
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)
| D: LYS30 ASP31 TYR33 ARG50 ASP52 GLU54 ASN55 ASN57 ILE59 PHE101 ASP102 THR103 ASN104 TYR106 E: TYR30 ASN32 PHE91 TRP92 GLY93 THR94 TRP97 F: THR6 VAL7 ALA8 PHE9 ASP10 ARG12 PRO13 GLY14 VAL16 HIS18 PHE20 HIS22 GLY40 GLY41 THR42 ASN43 GLN45 GLN47 ARG65 PRO66 |
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)
