SMTL ID : 2xzh.1

CLATHRIN TERMINAL DOMAIN COMPLEXED WITH PITSTOP 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

monomer

Ligands

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

VH2.1: 9 residues within 4Å: Chain A: V.51, I.53, I.63, R.65, I.81, F.92, I.94, K.99 Ligands: DMS.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.51, A:I.53, A:R.65, A:R.65, A:I.81, A:F.92, A:F.92, A:F.92 Hydrogen bonds: A:R.65, A:R.65

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

DMS.2: 5 residues within 4Å: Chain A: F.28, T.32, I.73, F.111, W.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.112 Water bridges: A:S.71 pi-Cation interactions: A:F.111 DMS.3: 4 residues within 4Å: Chain A: R.222, V.251, F.252, F.253 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.253 DMS.4: 8 residues within 4Å: Chain A: R.177, V.178, H.198, R.222, Q.258, N.259, D.260, F.261 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.178 DMS.5: 5 residues within 4Å: Chain A: I.67, Q.90, F.92, K.99 Ligands: VH2.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.90 pi-Cation interactions: A:F.92

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

ACT.6: 2 residues within 4Å: Chain A: H.146, S.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.147 Salt bridges: A:H.146 ACT.7: 3 residues within 4Å: Chain A: N.176, R.177, N.259 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.259 Water bridges: A:N.176, A:N.176 ACT.8: 2 residues within 4Å: Chain A: S.137, Q.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.136, A:Q.138, A:Q.138 ACT.9: 3 residues within 4Å: Chain A: K.141, M.142, F.143 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.141, A:K.141, A:K.141, A:Y.185 Salt bridges: A:K.141 ACT.10: 5 residues within 4Å: Chain A: M.100, K.101, A.102, G.135, E.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.102, A:A.102

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

EDO.11: 7 residues within 4Å: Chain A: S.68, L.83, K.84, A.85, T.88, L.89, Q.90 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.85, A:T.88 Water bridges: A:S.68 EDO.12: 4 residues within 4Å: Chain A: R.298, I.299, S.300, G.301 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain A: S.29, R.42, D.70, S.71 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.71 Water bridges: A:R.42, A:S.71 EDO.16: 3 residues within 4Å: Chain A: N.93, M.100, E.134 No protein-ligand interaction detected (PLIP) EDO.17: 3 residues within 4Å: Chain A: Q.15, Q.17, N.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.15 Water bridges: A:Q.15

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

PEG.14: 7 residues within 4Å: Chain A: Q.204, F.205, K.206, E.269, D.272, R.355, N.357 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.206, A:E.213, A:N.357 Water bridges: A:D.272, A:D.272 PEG.15: 4 residues within 4Å: Chain A: C.293, Y.295, M.296, Y.338 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.296, A:M.296, A:Y.338 Water bridges: A:C.293, A:C.293

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

2011-08-17

Peptides

CLATHRIN HEAVY CHAIN 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CLATHRIN HEAVY CHAIN 1