SMTL ID : 5xcx.1

Crystal structure of TS2/16 Fv-clasp fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

hetero-1-1-mer

Ligands

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

PO4.1: 2 residues within 4Å: Chain A: E.152, R.155 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.155 Salt bridges: A:R.155 PO4.2: 6 residues within 4Å: Chain A: S.53, S.54, G.55, G.56, S.57, Y.58 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.53, A:G.55, A:G.55, A:S.57, A:S.57 Water bridges: A:S.54 PO4.3: 3 residues within 4Å: Chain A: H.110, W.111 Chain B: K.50 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:K.50, A:H.110 Hydrogen bonds: A:W.111 Water bridges: A:D.109

2 x CXS: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID(Non-covalent)

CXS.4: 7 residues within 4Å: Chain A: Y.60, D.103, Y.106 Chain B: Y.37, G.96, S.97, I.99 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.37, B:I.99, B:I.99, A:Y.106 CXS.5: 4 residues within 4Å: Chain A: R.155, R.162 Chain B: L.132, M.139 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Water bridges: A:R.162, A:R.162 Salt bridges: A:R.155, A:R.162 Hydrophobic interactions: B:L.132

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: Y.102, D.109 Chain B: Y.54 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.101, A:D.105

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

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