SMTL ID : 4g55.1

Clathrin terminal domain complexed with pitstop 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

monomer

Ligands

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

DMS.1: 5 residues within 4Å: Chain A: F.32, T.36, I.77, F.115, W.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.116 Water bridges: A:S.75 pi-Cation interactions: A:F.115 DMS.2: 8 residues within 4Å: Chain A: R.181, V.182, H.202, R.226, Q.262, N.263, D.264, F.265 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.182 DMS.3: 5 residues within 4Å: Chain A: I.71, Q.94, F.96, K.103 Ligands: VH2.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.94, A:K.103 pi-Cation interactions: A:F.96 DMS.15: 4 residues within 4Å: Chain A: M.109, T.110, D.111, Y.133 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.130 Salt bridges: A:D.111

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

ACT.4: 2 residues within 4Å: Chain A: H.150, S.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.151 Salt bridges: A:H.150 ACT.5: 4 residues within 4Å: Chain A: N.180, R.181, Q.262, N.263 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.263 ACT.6: 2 residues within 4Å: Chain A: S.141, Q.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.140, A:Q.142, A:Q.142 ACT.7: 3 residues within 4Å: Chain A: K.145, M.146, F.147 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.145 Hydrogen bonds: A:K.145 Water bridges: A:Y.189 ACT.17: 4 residues within 4Å: Chain A: R.226, V.255, F.256, F.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.255, A:F.257

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

EDO.8: 6 residues within 4Å: Chain A: S.72, L.87, K.88, A.89, T.92, Q.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.89, A:T.92 EDO.9: 4 residues within 4Å: Chain A: R.302, I.303, S.304, G.305 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain A: N.97, M.104, M.137, E.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.97, A:M.137 EDO.13: 3 residues within 4Å: Chain A: Q.19, Q.21, N.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.19 Water bridges: A:Q.19 EDO.14: 5 residues within 4Å: Chain A: K.117, N.160, A.268, V.310, T.311 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.117, A:K.117, A:T.311 Water bridges: A:N.160, A:Q.270 EDO.16: 5 residues within 4Å: Chain A: M.104, K.105, A.106, G.139, E.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.106, A:A.106, A:E.140

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 8 residues within 4Å: Chain A: Q.208, F.209, K.210, E.217, E.273, D.276, R.359, N.361 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.210, A:E.217, A:N.361 Water bridges: A:E.273, A:D.276, A:D.276 PEG.11: 4 residues within 4Å: Chain A: C.297, Y.299, M.300, Y.342 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.300, A:M.300, A:Y.342

1 x VH2: N-[5-[(4-BROMOPHENYL)METHYL]-4-HYDROXY-1,3-THIAZOL-2-YL]NAPHTHALENE-1-SULFONAMIDE(Non-covalent)

VH2.18: 11 residues within 4Å: Chain A: V.55, I.57, I.67, R.69, I.71, I.85, F.96, I.98, K.101, K.103 Ligands: DMS.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.55, A:I.57, A:R.69, A:R.69, A:I.71, A:I.85, A:F.96, A:F.96, A:F.96 Hydrogen bonds: A:R.69, A:R.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

von Kleist, L. et al., Role of the clathrin terminal domain in regulating coated pit dynamics revealed by small molecule inhibition. Cell(Cambridge,Mass.) (2011)

Release Date

2012-08-01

Peptides

Clathrin heavy chain 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Clathrin heavy chain 1

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