SMTL ID : 5m5v.1 (1 other biounit)

Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

3 x LEU- PRO- LEU- LEU- GLU- SER: Large delta antigen(Non-covalent)

LEU-PRO-LEU-LEU-GLU-SER.1: 11 residues within 4Å: Chain A: R.66, P.67, I.68, S.69, L.84, K.85, A.86, T.89, Q.91, F.93, K.98 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:R.66, A:P.67, A:I.68, A:L.84, A:A.86, A:F.93, A:F.93 Hydrogen bonds: A:P.67, A:S.69, A:Q.91, A:Q.91 Water bridges: A:Q.49, A:S.69 LEU-PRO-LEU-LEU-GLU-SER.2: 10 residues within 4Å: Chain A: L.7, F.11, E.13, Y.296, N.298, R.299, I.300, S.301, G.302, Q.325 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.11, A:F.11, A:N.298, A:R.299 Hydrogen bonds: A:F.11, A:N.298, A:N.298, A:R.299, A:Q.325 Water bridges: A:E.13, A:I.300 Salt bridges: A:E.13 LEU-PRO-LEU-LEU-GLU-SER.3: 9 residues within 4Å: Chain A: W.166, L.185, S.187, R.190, V.192, Q.194, I.196, F.218, V.235 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.185, A:Q.194, A:I.196, A:F.218, A:F.218, A:V.235 Hydrogen bonds: A:Q.194, A:Q.194 Water bridges: A:R.190

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: H.104, M.106, T.107, D.108, Y.130 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.107, A:D.108, A:D.108, A:D.108 Water bridges: A:H.104, A:H.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muenzner, J. et al., Cellular and viral peptides bind multiple sites on the N-terminal domain of clathrin. Traffic (2017)

Release Date

2016-11-23

Peptides

Clathrin heavy chain 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Clathrin heavy chain 1

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