SMTL ID : 3w15.1

Structure of peroxisomal targeting signal 2 (PTS2) of Saccharomyces cerevisiae 3-ketoacyl-CoA thiolase in complex with Pex7p and Pex21p

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-oligomer

Ligands

9 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 6 residues within 4Å: Chain A: E.151, I.152, Y.200, L.218 Chain C: D.60, K.65 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Y.200, C:K.65, C:K.65 NO3.2: 5 residues within 4Å: Chain A: R.25, I.44, V.56, N.57, T.92 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.25, A:R.25, A:N.57 Water bridges: A:T.92 NO3.4: 3 residues within 4Å: Chain B: H.96, K.97, I.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.97 NO3.5: 5 residues within 4Å: Chain C: N.31, K.34, W.81, A.82, L.281 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.34, C:A.82 Water bridges: C:N.31 NO3.6: 5 residues within 4Å: Chain C: Y.261, G.262, V.263, P.334, R.335 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.263 Water bridges: C:Y.136, C:Y.136, C:V.263 NO3.7: 6 residues within 4Å: Chain C: Y.186, A.187, F.188, F.277, E.347, P.350 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.187, C:F.188 Water bridges: C:Y.195 NO3.8: 5 residues within 4Å: Chain C: K.159, K.221, H.222, M.223, N.224 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.159, C:M.223 Water bridges: C:N.224 NO3.9: 4 residues within 4Å: Chain C: P.248, W.251, P.317, G.319 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:P.248, C:R.335 Water bridges: C:W.251, C:G.319 NO3.10: 3 residues within 4Å: Chain C: N.31, G.32, D.33 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.31, C:G.32, C:D.33 Water bridges: C:N.31

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 5 residues within 4Å: Chain A: D.67, L.68, A.69, C.112, N.113 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.67, A:L.68, A:C.112, H2O.1, H2O.1 MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain C: D.74 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.74, H2O.7, H2O.7, H2O.7, H2O.7, H2O.7 MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain C: D.228 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.228, H2O.12, H2O.12, H2O.12, H2O.12, H2O.12 MG.15: 1 residues within 4Å: Chain C: E.63 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, D. et al., Crystal structure of peroxisomal targeting signal-2 bound to its receptor complex Pex7p-Pex21p. Nat.Struct.Mol.Biol. (2013)

Release Date

2013-07-03

Peptides

Peroxisomal targeting signal 2 receptor: A
Peroxisomal membrane protein PEX21: B
3-ketoacyl-CoA thiolase, peroxisomal, Maltose-binding periplasmic protein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Peroxisomal targeting signal 2 receptor

Peroxisomal membrane protein PEX21

3-ketoacyl-CoA thiolase, peroxisomal, Maltose-binding periplasmic protein