SMTL ID : 6rt2.2 (3 other biounits)

Crystal structure of Trypanosoma Brucei PEX14 N-terminal domain in complex with small molecules designed to investigate the water envelope

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x CV5: (3~{S})-3-[[1-(2-hydroxyethyl)-5-[(4-methoxynaphthalen-1-yl)methyl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-3-yl]carbonylamino]-3-phenyl-propanoic acid(Non-covalent)

CV5.1: 13 residues within 4Å: Chain A: N.14, A.15, E.17, F.18, D.21, R.23, V.24, T.27, S.31, F.35, L.36, K.39, L.41 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:N.14, A:D.21, A:R.23, A:V.24, A:L.36, A:K.39, A:L.41 Water bridges: A:N.14, A:F.18, A:D.21 pi-Stacking: A:F.18, A:F.18, A:F.35

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: S.42, A.43 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.43 Water bridges: A:K.37, A:E.44 Salt bridges: A:K.37 SO4.3: 3 residues within 4Å: Chain A: P.28, T.29, K.57 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.29, A:T.29, A:T.29 Water bridges: A:S.30, A:K.32, A:K.57 Salt bridges: A:K.57 SO4.4: 3 residues within 4Å: Chain A: T.58, N.60, R.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.58, A:E.61 Salt bridges: A:R.64

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.5: 2 residues within 4Å: Chain A: C.47, E.48 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ratkova, E.L. et al., Water envelope has a critical impact on the design of protein-protein interaction inhibitors. Chem.Commun.(Camb.) (2020)

Release Date

2020-04-08

Peptides

Peroxin 14: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Peroxin 14

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