SMTL ID : 5yd3.2 (3 other biounits)

Crystal structure of the scFv antibody 4B08 with epitope peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

1 x ILE- ASN- TYR- TYR- THR- SER- GLU- PRO: Epitope peptide(Non-covalent)

ILE-ASN-TYR-TYR-THR-SER-GLU-PRO.1: 15 residues within 4Å: Chain A: T.30, W.33, D.50, H.52, S.55, Y.57, N.59, D.99, H.169, Y.175, H.234, L.235, E.236, Y.237, Y.239 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.175, A:Y.175, A:Y.237 Hydrogen bonds: A:D.50, A:S.55, A:N.59, A:Y.237, A:Y.237, A:Y.237, A:Y.237, A:Y.239 Water bridges: A:N.171 Salt bridges: A:H.169 pi-Stacking: A:Y.57

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: Y.27, T.28, K.31, Y.32 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.28, A:T.28, A:T.28, A:Y.32 Water bridges: A:R.98 Salt bridges: A:K.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyanabe, K. et al., Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody. J. Biochem. (2018)

Release Date

2018-06-06

Peptides

scFv 4B08: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

scFv 4B08

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