5M5S Endocytosis date Oct 22, 2016
title Clathrin Heavy Chain N-Terminal Domain Bound To Amphiphysin Box Motif
authors J.Muenzner, S.C.Graham
compound source
Molecule: Clathrin Heavy Chain 1
Chain: A, B
Engineered: Yes
Other_details: N-Terminal Residues 'Gs' Are Residual Follow Cleavage Of The Purification Tag;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Gene: Cltc
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Popt3g

Molecule: Amphiphysin
Chain: E, F, G, H
Fragment: Clathrin-Box Motif, Unp Residues 349-358
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: C 1 2 1
R_factor 0.204 R_Free 0.234
length a length b length c angle alpha angle beta angle gamma
139.967 134.110 78.012 90.00 115.07 90.00
method X-Ray Diffractionresolution 1.88 Å
ligand GOL enzyme
A, B

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (265 Kb) [Save to disk]
  • Biological Unit Coordinates (5m5s.pdb1.gz) 131 Kb
  • Biological Unit Coordinates (5m5s.pdb2.gz) 132 Kb
  • LPC: Ligand-Protein Contacts for 5M5S
  • CSU: Contacts of Structural Units for 5M5S
  • Structure Factors (2371 Kb)
  • Retrieve 5M5S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5M5S from S2C, [Save to disk]
  • Re-refined 5m5s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5M5S in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5M5S
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5m5s from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5m5s_A] [5m5s] [5m5s_E] [5m5s_G] [5m5s_B] [5m5s_F] [5m5s_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5M5S
  • Community annotation for 5M5S at PDBWiki (http://pdbwiki.org)

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