5C5A Ligase date Jun 19, 2015
title Crystal Structure Of Hdm2 In Complex With Nutlin-3a
authors J.Orts, M.A.Waelti, M.Marsh, L.Vera, A.D.Gossert, P.Guentert, R.Ri
compound source
Molecule: E3 Ubiquitin-Protein Ligase Mdm2
Chain: A, B
Synonym: Double Minute 2 Protein,Hdm2,Oncoprotein Mdm2,P53- Protein Mdm2;
Ec: 6.3.2.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mdm2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: P 1 21 1
R_factor 0.153 R_Free 0.168
length a length b length c angle alpha angle beta angle gamma
41.620 43.630 52.670 90.00 90.04 90.00
method X-Ray Diffractionresolution 1.15 Å
ligand CL, IOD, NUT, SO4 enzyme Ligase E.C.6.3.2 BRENDA
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (111 Kb) [Save to disk]
  • Biological Unit Coordinates (5c5a.pdb1.gz) 53 Kb
  • Biological Unit Coordinates (5c5a.pdb2.gz) 53 Kb
  • LPC: Ligand-Protein Contacts for 5C5A
  • CSU: Contacts of Structural Units for 5C5A
  • Structure Factors (762 Kb)
  • Retrieve 5C5A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5C5A from S2C, [Save to disk]
  • Re-refined 5c5a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5C5A 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 5C5A
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5c5a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5c5a] [5c5a_A] [5c5a_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5C5A
  • Community annotation for 5C5A at PDBWiki (http://pdbwiki.org)

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