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Entry information

Complex
AACDB_ID: 1238
PDBID: 5CZX
Chains: HL_A
Organism: Homo sapiens
Method: XRD
Resolution (Å): 2.10
Reference: 10.1038/onc.2016.133
Antibody
Antibody: 20358 Fab
Antibody mutation: No
INN (Clinical Trial):
Antigen
Antigen: Neurogenic locus notch homolog protein 3
Antigen mutation: No
Durg Target:

Sequence information

Antibody

Heavy Chain: H
Mutation: NULL

>5CZX_H|Chain C, E[auth H]|20358 Fab heavy chain|Homo sapiens (9606)
QVQLVQSGAEVKKPGSSVKVSCKASGGTFRTYAMHWVRQAPGQGLEWMGGIVPYHGITDYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARDDYSTYAFAYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

Light Chain: L
Mutation: NULL

>5CZX_L|Chain D, F[auth L]|20358 Fab light chain|Homo sapiens (9606)
DIQMTQSPSSLSASVGDRVTITCRASQSIASYLAWYQQKPGKAPKLLIYDASNLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQAYKTPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Antigen

Chain: A
Mutation: NULL

>5CZX_A|Chain A, B|Neurogenic locus notch homolog protein 3|Homo sapiens (9606)
APEVSEEPRCPRAACQAKRGDQRCDRECNSPGCGWDGGDCSLSVGDPWRQCEALQCWRLFNNSRCDPACSSPACLYDNFDCHAGGRERTCNPVYEKYCADHFADGRCDQGCNTEECGWDGLDCASEVPALLARGVLVLTVLLPPEELLRSSADFLQRLSAILRTSLRFRLDAHGQAMVFPYHRPSPGSEPRARRELAPEVIGSVVMLEIDNRLCLQSPENDHCFPDAQSAADYLGALSAVERLDFPYPLRDVRGEPLEPPEPSGSHHHHHH

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: PHE29 THR31 ALA33 HIS35 TRP47 GLY50 ILE51 VAL52 HIS55 ILE57 THR58 ASP59 ASP99 ASP100 TYR101 SER102 THR103 TYR104

L: GLN27 SER28 ALA30 SER31 TYR32 SER67 ALA91 TYR92 LYS93 THR94 TYR96

A: ASN1438 SER1440 GLY1462 ARG1463 ARG1465 THR1466 ASN1468 PRO1469 VAL1470 TYR1471 GLU1472 LYS1473 TYR1474 GLN1486 GLY1487 ARG1534 GLU1618 ARG1619 ASP1621

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)

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