SMTL ID : 9exg.2 (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: 19 residues within 4Å: Chain A: V.53, 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, L.97, K.100, S.101, K.102 Ligands: PO4.5 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.53, A:K.67, A:M.69, A:V.85, A:F.95, A:F.95, A:F.95, A:L.97 Hydrogen bonds: A:K.67, A:N.68, A:G.70, A:G.71, A:Q.93, A:Q.93, A:K.102 Water bridges: A:N.68, A:N.68 Salt bridges: A:K.67, A:K.100 GLY-VAL-SER-LEU-ILE-ASP-LEU.2: 15 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 Ligands: GOL.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.30, A:I.161, A:I.177, A:Q.179, A:I.184, A:I.272, 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 Water bridges: A:D.29, A:S.312, A:K.330 Salt bridges: A:K.288, A:K.330 GLY-VAL-SER-LEU-ILE-ASP-LEU.3: 10 residues within 4Å: Chain A: W.171, L.190, I.197, Q.199, I.201, F.224, T.226, R.239, I.241, K.255 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.197, A:F.224, A:R.239, A:I.241, A:I.241 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: F.30, R.116, I.161, N.162, I.272, A.273, Q.275, T.315, A.316 Ligands: SER-LEU-ILE-ASP-LEU.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.116, A:T.315, A:A.316 Water bridges: A:N.162, A:N.162

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 5 residues within 4Å: Chain A: Q.93, K.102, S.105 Ligands: GLY-VAL-SER-LEU-ILE-ASP-LEU.1, GLY-VAL-SER-LEU-ILE-ASP-LEU.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.93, A:S.105 Salt bridges: A:K.102

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
B

Clathrin heavy chain

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