SMTL ID : 5xct.1

Crystal structure of P20.1 Fv-clasp fragment with its antigen peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLY- TYR- PRO- GLY- GLN- VAL: C8 peptide(Non-covalent)

GLY-TYR-PRO-GLY-GLN-VAL.1: 16 residues within 4Å: Chain A: T.31, T.32, A.33, G.34, Q.36, W.51, N.53, T.54, R.55, E.100, G.101, P.102, G.103 Chain B: Y.36, W.95, W.100 19 PLIP interactions: 12 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:P.102, B:Y.36, B:W.95, B:W.100 Hydrogen bonds: A:G.34, A:Q.36, A:T.54, A:T.54, A:T.54, A:R.55, A:E.100, A:E.100, A:E.100, A:G.103 Water bridges: A:N.53, B:Y.36, B:Y.36 pi-Stacking: B:W.95, B:W.95

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

CL.2: 1 residues within 4Å: Chain A: K.134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arimori, T. et al., Fv-clasp: An Artificially Designed Small Antibody Fragment with Improved Production Compatibility, Stability, and Crystallizability. Structure (2017)

Release Date

2017-10-04

Peptides

VH(S112C)-SARAH chimera: A
VL-SARAH(S37C)chimera: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

VH(S112C)-SARAH chimera

VL-SARAH(S37C)chimera