SMTL ID : 6e4l.1

The structure of the N-terminal domain of human clathrin heavy chain 1 (nTD) in complex with ES9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 7 residues within 4Å: Chain A: F.32, S.33, T.36, S.75, I.77, F.115, W.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.116 DMS.2: 8 residues within 4Å: Chain A: R.181, V.182, R.226, G.227, Q.262, N.263, D.264, F.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.182 Water bridges: A:N.263

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: K.117, N.160, R.162, A.203, A.204, A.268, M.269, Q.270, V.310, T.311 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.162, A:M.269, A:M.269, A:T.311, A:T.311 Water bridges: A:K.117, A:N.160, A:F.309

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 2 residues within 4Å: Chain A: E.306, R.325 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.325 Water bridges: A:E.306, A:E.306 EDO.5: 6 residues within 4Å: Chain A: K.145, M.146, F.147, D.148, Y.189, K.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.189

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 8 residues within 4Å: Chain A: F.42, I.57, D.59, I.67, R.69, M.78, K.83, I.98 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.42 Salt bridges: A:R.69 ACT.7: 7 residues within 4Å: Chain A: Q.208, F.209, K.210, E.217, E.273, K.274, D.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.210 Water bridges: A:D.276 ACT.8: 4 residues within 4Å: Chain A: R.302, I.303, S.304, G.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.302 Water bridges: A:G.305 Salt bridges: A:R.302

1 x HRS: 5-bromo-N-(4-nitrophenyl)thiophene-2-sulfonamide(Non-covalent)

HRS.9: 11 residues within 4Å: Chain A: R.69, I.71, S.72, A.73, I.85, L.87, K.88, A.89, Q.94, F.96, I.98 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.71, A:I.71, A:L.87 pi-Stacking: A:F.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dejonghe, W. et al., Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. Nat.Chem.Biol. (2019)

Release Date

2019-04-24

Peptides

Clathrin heavy chain 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Clathrin heavy chain 1

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