SMTL ID : 9exf.1 (4 other biounits)

Crystal structure of Yeast Clathrin Heavy Chain N-terminal domain bound to YAP1801 peptide (LIDM)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

2 x ASN- LEU- ASN- LEU- ILE- ASP- MET: Clathrin coat assembly protein AP180A(Non-covalent)

ASN-LEU-ASN-LEU-ILE-ASP-MET.1: 17 residues within 4Å: Chain A: W.171, L.190, F.191, S.192, R.195, I.197, S.198, Q.199, I.201, D.202, F.224, T.226, R.239, I.241, E.242, I.243, K.255 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.171, A:W.171, A:L.190, A:I.197, A:I.197, A:F.224 Hydrogen bonds: A:Q.199, A:Q.199, A:Q.199, A:K.255 Salt bridges: A:K.255 ASN-LEU-ASN-LEU-ILE-ASP-MET.2: 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, N.96, L.97, K.100, S.101, K.102 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:M.69, A:I.83, A:V.85, A:I.91, A:F.95 Hydrogen bonds: A:N.68, A:G.70, A:G.71, A:Q.93, A:Q.93, A:K.102 Water bridges: A:N.68 Salt bridges: A:K.67

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: F.30, R.116, I.161, N.162, I.272, A.273, V.274, Q.275, F.314, T.315, A.316 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.116, A:Q.275, A:T.315, A:A.316 Water bridges: A:R.116, A:R.116, A:N.162

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
A

Clathrin heavy chain

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