SMTL ID : 9exf.5 (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

homo-tetramer

Ligands

10 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: 16 residues within 4Å: Chain B: 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 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.171, B:L.190, B:I.197, B:I.201, B:I.241, B:I.243 Hydrogen bonds: B:Q.199, B:Q.199, B:Q.199, B:K.255 Water bridges: B:R.239 Salt bridges: B:R.239, B:K.255 ASN-LEU-ASN-LEU-ILE-ASP-MET.3: 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 ASN-LEU-ASN-LEU-ILE-ASP-MET.4: 17 residues within 4Å: Chain D: 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 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:W.171, D:W.171, D:L.190, D:L.190, D:I.197, D:I.197, D:F.224, D:I.241, D:I.243 Hydrogen bonds: D:Q.199, D:Q.199, D:Q.199, D:K.255 Salt bridges: D:K.255 ASN-LEU-ASN-LEU-ILE-ASP-MET.5: 19 residues within 4Å: Chain B: T.46, G.49 Chain C: 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, K.102 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:M.69, C:V.85, C:A.87, C:I.91, B:T.46 Hydrogen bonds: C:G.70, C:Q.93, C:Q.93, C:K.100, C:K.102 Salt bridges: C:K.67 ASN-LEU-ASN-LEU-ILE-ASP-MET.6: 16 residues within 4Å: Chain D: V.53, I.55, K.67, N.68, M.69, G.70, I.83, V.85, R.86, A.87, I.91, V.92, Q.93, F.95, L.97, K.102 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:M.69, D:I.83, D:V.85, D:A.87, D:F.95 Hydrogen bonds: D:N.68, D:G.70, D:Q.93, D:Q.93, D:K.102 Salt bridges: D:K.67 ASN-LEU-ASN-LEU-ILE-ASP-MET.7: 19 residues within 4Å: Chain B: V.53, K.67, N.68, M.69, G.70, I.83, V.85, R.86, A.87, I.91, V.92, Q.93, F.95, L.97, K.102 Chain C: T.46, K.47, D.48, G.49 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:M.69, B:V.85, B:F.95, C:K.47 Hydrogen bonds: B:N.68, B:G.70, B:Q.93, B:K.102, C:D.48, C:D.48, C:G.49 ASN-LEU-ASN-LEU-ILE-ASP-MET.8: 14 residues within 4Å: Chain D: 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 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.30, D:I.161, D:I.177, D:Q.179, D:I.272, D:F.314 Hydrogen bonds: D:F.30, D:Q.159, D:K.288 Salt bridges: D:K.330 ASN-LEU-ASN-LEU-ILE-ASP-MET.9: 23 residues within 4Å: Chain B: P.111, I.113, A.128, R.129, N.157, T.158 Chain C: D.29, F.30, R.31, N.157, T.158, Q.159, I.161, I.177, L.178, Q.179, I.184, F.270, I.272, K.288, F.314, K.330 Ligands: LEU-ASN-LEU-ILE-ASP-MET.10 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.30, C:I.161, C:I.177, C:Q.179, C:I.272, C:F.314 Hydrogen bonds: C:F.30, C:R.31, C:Q.159, C:Q.159, C:K.288 Salt bridges: C:K.330 ASN-LEU-ASN-LEU-ILE-ASP-MET.10: 21 residues within 4Å: Chain B: D.29, F.30, R.31, N.157, Q.159, I.161, I.177, L.178, Q.179, I.184, F.270, I.272, K.288, F.314, K.330 Chain C: I.113, A.128, R.129, N.157, T.158 Ligands: LEU-ASN-LEU-ILE-ASP-MET.9 13 PLIP interactions: 2 interactions with chain C, 11 interactions with chain B Hydrogen bonds: C:R.129, C:R.129, B:F.30, B:R.31, B:Q.159, B:Q.159, B:Q.159, B:K.288 Hydrophobic interactions: B:F.30, B:I.161, B:I.177, B:Q.179 Salt bridges: B:K.330

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 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

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 3 residues within 4Å: Chain C: R.239, K.255, T.257 Ligand excluded by PLIP

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Clathrin heavy chain

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