SMTL ID : 5yd5.1 (1 other biounit)

Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation N3A)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

1 x ILE- ALA- TYR- TYR- THR- SER- GLU- PRO: Peptide epitope (mutation N3A)(Non-covalent)

ILE-ALA-TYR-TYR-THR-SER-GLU-PRO.1: 17 residues within 4Å: Chain A: K.31, Y.32, W.33, D.50, H.52, S.55, Y.57, D.99, Y.101, T.102, H.169, Y.175, H.234, L.235, E.236, Y.237, Y.239 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.32, A:Y.57, A:Y.101, A:Y.101, A:Y.175, A:Y.237 Hydrogen bonds: A:D.50, A:S.55, A:Y.237, A:Y.237, A:Y.237, A:Y.239 Water bridges: A:D.99, A:H.169, A:R.170 Salt bridges: A:H.169

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

SO4.2: 3 residues within 4Å: Chain A: R.13, G.120, G.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.121 Salt bridges: A:R.13 SO4.3: 5 residues within 4Å: Chain A: S.17, S.84, G.125, G.126, S.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.17, A:G.126 SO4.4: 3 residues within 4Å: Chain A: S.156, R.217, S.219 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.156, A:S.219 Salt bridges: A:R.217 SO4.5: 4 residues within 4Å: Chain A: Y.27, T.28, K.31, Y.32 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.28 Water bridges: A:R.98, A:R.98 Salt bridges: A:K.31 SO4.6: 2 residues within 4Å: Chain A: S.116, S.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.117

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
A

scFv 4B08

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