SMTL ID : 5lyn.1

Structure of the Tpr Domain of Sgt2 in complex with yeast Ssa1 peptide fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x PRO- THR- VAL- GLU- GLU- VAL- ASP: PRO-THR-VAL-GLU-GLU-VAL-ASP(Non-covalent)

PRO-THR-VAL-GLU-GLU-VAL-ASP.1: 13 residues within 4Å: Chain B: K.14, N.18, M.21, Y.33, N.49, A.52, Y.77, R.79, S.82, R.83, F.86, A.115, D.119 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.52 Hydrogen bonds: B:N.18, B:N.49, B:N.49, B:R.83, B:R.83, B:D.119, B:D.119, A:E.114 Water bridges: B:Y.77, B:R.79, B:R.79, B:R.79 Salt bridges: B:K.14, B:R.79 PRO-THR-VAL-GLU-GLU-VAL-ASP.2: 18 residues within 4Å: Chain A: K.14, N.18, M.21, Y.33, I.45, N.49, A.52, S.55, S.56, R.79, S.82, R.83, F.86, Y.89, Y.101, D.119, S.122 Ligands: ZN.11 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.86, A:F.86 Hydrogen bonds: A:N.18, A:N.49, A:N.49, A:S.82, A:R.83, A:R.83 Water bridges: A:D.119 Salt bridges: A:K.14, A:R.79

9 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.3: 1 residues within 4Å: Chain A: D.25 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.25 ZN.4: 2 residues within 4Å: Chain A: E.108 Chain B: E.108 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.108, A:E.108, A:E.108, H2O.3, H2O.3 ZN.5: 2 residues within 4Å: Chain A: K.32, E.35 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.35, A:E.35, H2O.3 ZN.6: 1 residues within 4Å: Chain A: L.133 No protein-ligand interaction detected (PLIP) ZN.7: 2 residues within 4Å: Chain A: D.74 Chain B: D.110 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.110, A:D.74, H2O.2, H2O.5, H2O.6 ZN.8: 1 residues within 4Å: Chain B: D.25 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.25, H2O.4, H2O.4 ZN.9: 2 residues within 4Å: Chain B: K.32, E.35 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.35, B:E.35, H2O.5 ZN.10: 2 residues within 4Å: Chain B: G.1, S.2 No protein-ligand interaction detected (PLIP) ZN.11: 1 residues within 4Å: Ligands: PRO-THR-VAL-GLU-GLU-VAL-ASP.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krysztofinska, E.M. et al., Structure and Interactions of the TPR Domain of Sgt2 with Yeast Chaperones and Ybr137wp. Front Mol Biosci (2017)

Release Date

2017-10-25

Peptides

Small glutamine-rich tetratricopeptide repeat-containing protein 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Small glutamine-rich tetratricopeptide repeat-containing protein 2