Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6786 |
| PDBID: | 4D9R |
| Chains: | ED_B |
| Organism: | Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.42 |
| Reference: | 10.1074/jbc.M112.345082 |
| Antibody | |
| Antibody: | AFD Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | Lampalizumab(Phase-III) |
| Antigen | |
| Antigen: | Macaca mulatta Factor D |
| Antigen mutation: | No |
| Durg Target: | P00746 |
Sequence information
Antibody
Heavy Chain: E
Mutation: NULL
| >4D9R_E|Chain C[auth E], E[auth H]|Fab heavy chain|Homo sapiens (9606) EVQLVQSGPELKKPGASVKVSCKASGYTFTNYGMNWVRQAPGQGLEWMGWINTYTGETTYADDFKGRFVFSLDTSVSTAYLQISSLKAEDTAVYYCEREGGVNNWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC |
Light Chain: D
Mutation: NULL
| >4D9R_D|Chain B[auth D], F[auth L]|Fab light chain|Homo sapiens (9606) DIQVTQSPSSLSASVGDRVTITCITSTDIDDDMNWYQQKPGKVPKLLISGGNTLRPGVPSRFSGSGSGTDFTLTISSLQPEDVATYYCLQSDSLPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: B
Mutation: NULL
| >4D9R_B|Chain A, D[auth B]|Complement factor D|Homo sapiens (9606) ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLA |
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)
| E: THR28 THR30 ASN31 TYR32 GLY33 TRP50 ASN52 TYR54 THR55 GLU57 GLU97 GLU99 GLY100 GLY101 ASN109 D: ASP30 ASP32 ASN34 TYR36 LEU46 SER49 ARG55 LEU89 SER91 ASP92 SER93 LEU94 TYR96 B: ASP129 VAL130 PRO132 ASP164 ARG165 ALA166 THR167 ASN169 THR170 ASP173 GLY174 ILE176 THR177 GLU178 LYS223 LYS224 |
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)
