SMTL ID : 5yy4.1

Crystal structure of the scFv antibody 4B08 with sulfated epitope peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

1 x ILE- ASN- TYS- TYS- THR- SER- GLU- PRO: C-C chemokine receptor type 5(Non-covalent)

ILE-ASN-TYS-TYS-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, N.59, D.99, Y.101, H.169, Y.175, H.234, L.235, E.236, Y.237, Y.239 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.32, A:Y.101, 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:W.33, A:D.50, A:H.169 Salt bridges: A:H.169 pi-Stacking: A:Y.57

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

SO4.2: 4 residues within 4Å: Chain A: Y.27, T.28, K.31, Y.32 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.28, A:T.28, A:T.28, A:Y.32 Salt bridges: A:K.31 SO4.3: 4 residues within 4Å: Chain A: S.208, G.209, S.210, R.217 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.208 Water bridges: A:S.208, A:T.215, A:T.215, A:T.215, A:R.217, A:R.217, A:R.217 Salt bridges: A:R.217

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: G.136, G.137, S.138 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyanabe, K. et al., Tyrosine Sulfation Restricts the Conformational Ensemble of a Flexible Peptide, Strengthening the Binding Affinity for an Antibody. Biochemistry (2018)

Release Date

2018-07-18

Peptides

scFv 4B08: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

scFv 4B08