SMTL ID : 3cvn.1

Structure of Peroxisomal Targeting Signal 1 (PTS1) binding domain of Trypanosoma brucei Peroxin 5 (TbPEX5)complexed to T. brucei Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) PTS1 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ARG- ALA- ALA- LYS- LEU: T. brucei GAPDH PTS1 peptide Ac-DRDAAKL(Non-covalent)

ARG-ALA-ALA-LYS-LEU.1: 19 residues within 4Å: Chain A: E.69, V.97, T.100, N.101, N.183, N.210, K.211, A.214, T.215, A.217, N.218, Y.229, R.241, Y.244, N.245, V.248, F.291 Ligands: EDO.3, EDO.23 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.97, A:T.100, A:A.214, A:A.217 Hydrogen bonds: A:N.101, A:N.101, A:N.210, A:N.218, A:N.218, A:Y.244, A:Y.244, A:N.245, A:N.245 Water bridges: A:N.252 Salt bridges: A:R.241 pi-Cation interactions: A:F.291

22 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: N.16, P.17, Y.18, L.42, E.45, A.46 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: D.290, F.291, M.294 Ligands: ARG-ALA-ALA-LYS-LEU.1 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: E.53, R.54, E.55, E.56 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: L.63, A.94, V.97, Q.207, K.211 Ligands: EDO.6, EDO.8, EDO.9 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain A: V.97, Q.173, A.176, S.177, V.180, K.211 Ligands: EDO.5, EDO.7, EDO.8 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: A.93, A.96, V.97, L.112, W.115, S.177, V.180 Ligands: EDO.6 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: Q.173, D.205, Q.207, L.208, K.211 Ligands: EDO.5, EDO.6, EDO.9 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: I.89, A.90, A.93, W.115, Q.173 Ligands: EDO.5, EDO.8 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: I.75, N.79, H.99 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: E.283, A.284, R.286, S.287 Ligands: EDO.20 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: L.109, A.110, R.113, E.153, E.156, C.157 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: H.103, N.183, L.184, N.186, Y.188 Ligand excluded by PLIP EDO.14: 1 residues within 4Å: Chain A: P.203 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: R.196, W.209, L.212, E.224, D.227, A.228 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: L.32, A.35, N.36, L.37, N.236, G.238 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: P.120, E.123 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: A.217, N.218, N.220 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: K.70, D.71, G.72, L.73 Ligands: EDO.20 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain A: E.69, K.70, D.71, E.102, R.241 Ligands: EDO.11, EDO.19 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: P.86, L.117, S.118 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain A: R.82, H.92, L.95, A.107, A.110, S.111, A.114 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain A: A.66, E.67, V.97, Q.207, N.210, Y.239, R.241 Ligands: ARG-ALA-ALA-LYS-LEU.1 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sampathkumar, P. et al., Structural Insights into the recognition of peroxisomal targeting signal 1 by Trypanosoma brucei peroxin 5. J.Mol.Biol. (2008)

Release Date

2008-06-24

Peptides

Peroxisome targeting signal 1 receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peroxisome targeting signal 1 receptor

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