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SMTL ID : 8c2g.1

14-3-3 sigma with Pin1 binding site pS72 and covalently bound CV1040

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-2-2-mer

Ligands

2 x T85: 2-iodanyl-4-(2-phenylimidazol-1-yl)benzaldehyde(Covalent)

T85.1:	11 residues within 4Å: Chain A: C.43, N.47, S.50, E.120, F.124, K.127, P.172, I.173, G.176, I.224 Chain B: W.13 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:K.127, A:I.173, A:I.224, B:W.13 Halogen bonds: A:S.50 pi-Stacking: B:W.13, B:W.13
T85.4:	11 residues within 4Å: Chain C: C.43, N.47, S.50, E.120, F.124, K.127, P.172, I.173, G.176, I.224 Chain D: W.13 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:W.13, C:K.127, C:I.173, C:I.224 pi-Stacking: D:W.13, D:W.13 Halogen bonds: C:S.50

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2:	1 residues within 4Å: Chain A: E.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.7, H₂O.2, H₂O.4
MG.3:	2 residues within 4Å: Chain A: E.40, E.115 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.40, A:E.40, A:E.115, H₂O.7
MG.5:	1 residues within 4Å: Chain C: E.7 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.7, H₂O.11, H₂O.13
MG.6:	2 residues within 4Å: Chain C: E.40, E.115 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.40, C:E.40, C:E.115, H₂O.16

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Verhoef, C.J.A. et al., Tracking the mechanism of covalent molecular glue stabilization using native mass spectrometry. Chem Sci (2023)

Release Date

2023-06-14

Peptides

14-3-3 protein sigma: AC
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
P

D
P

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

14-3-3 protein sigma

Toggle Identical (AC)

Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1

Toggle Identical (BD)

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