SMTL ID : 9exg.3 (2 other biounits)

Crystal structure of Yeast Clathrin Heavy Chain N-terminal domain bound to Epsin-2 peptide (LIDL)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

3 x GLY- VAL- SER- LEU- ILE- ASP- LEU: Epsin-2(Non-covalent)

GLY-VAL-SER-LEU-ILE-ASP-LEU.1: 14 residues within 4Å: Chain A: D.29, F.30, R.31, Q.159, I.161, I.177, L.178, Q.179, I.184, F.270, I.272, K.288, F.314, K.330 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.30, A:F.30, A:I.161, A:I.177, A:F.314 Hydrogen bonds: A:F.30, A:R.31, A:R.31, A:Q.159, A:Q.159, A:Q.159, A:K.288 Salt bridges: A:K.288, A:K.330 GLY-VAL-SER-LEU-ILE-ASP-LEU.2: 18 residues within 4Å: Chain A: V.53, I.55, K.67, N.68, M.69, G.70, G.71, I.83, V.85, R.86, A.87, I.91, V.92, Q.93, F.95, N.96, L.97, K.100 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.67, A:I.83, A:V.85, A:F.95, A:F.95, A:L.97 Hydrogen bonds: A:N.68, A:G.70, A:G.71, A:Q.93, A:Q.93 Water bridges: A:N.68, A:N.68, A:K.102 Salt bridges: A:K.100 GLY-VAL-SER-LEU-ILE-ASP-LEU.3: 16 residues within 4Å: Chain A: W.171, L.190, F.191, S.192, R.195, I.197, S.198, Q.199, I.201, F.224, T.226, R.239, I.241, E.242, I.243, K.255 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.171, A:L.190, A:I.197, A:Q.199, A:I.201, A:I.201, A:F.224, A:R.239, A:I.241, A:I.243 Hydrogen bonds: A:Q.199, A:Q.199, A:Q.199, A:K.255 Water bridges: A:R.239 Salt bridges: A:R.239, A:K.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Defelipe, L.A. et al., Subtleties in Clathrin heavy chain binding boxes provide selectivity among adaptor proteins of budding yeast. Nat Commun (2024)

Release Date

2024-11-13

Peptides

Clathrin heavy chain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Clathrin heavy chain

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