SMTL ID : 6lcs.1

Crystal structure of 73MuL9 Fv-clasp fragment in complex with GA-pyridine analogue

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

1 x E9R: (2~{S})-6-[4-(hydroxymethyl)-3-oxidanyl-pyridin-1-ium-1-yl]-2-(phenylmethoxycarbonylamino)hexanoic acid(Non-covalent)

E9R.1: 9 residues within 4Å: Chain A: Y.34, N.36, Y.48, Y.51, P.99, Y.105 Chain B: Q.91, S.93, Y.98 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.34, A:P.99, A:Y.105, A:Y.105, A:Y.105 Hydrogen bonds: A:N.36, A:Y.48, B:Q.91, B:Q.91 pi-Stacking: B:Y.98

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 3 residues within 4Å: Chain A: Y.54, S.55, R.57 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.54, A:Y.54, A:Y.54, A:S.55 Salt bridges: A:R.57 PO4.3: 3 residues within 4Å: Chain A: Y.100, Y.101, R.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.100 Salt bridges: A:R.102 PO4.4: 2 residues within 4Å: Chain B: S.31, S.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kobashigawa, Y. et al., Molecular recognition of a single-chain Fv antibody specific for GA-pyridine, an advanced glycation end-product (AGE), elucidated using biophysical techniques and synthetic antigen analogues. J.Biochem. (2021)

Release Date

2020-11-25

Peptides

VH-SARAH: A
VL-SARAH: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

VH-SARAH

VL-SARAH