3LNJ Ligase Ligase Inhibitor date Feb 02, 2010
title Crystal Structure Of Human Mdm2 In Complex With D-Peptide In (Dpmi-Alpha)
authors M.Pazgier, W.Lu
compound source
Molecule: E3 Ubiquitin-Protein Ligase Mdm2
Chain: A, C, E
Fragment: Unp Residues 25-109, P53 Binding Domain
Synonym: P53-Binding Protein Mdm2, Oncoprotein Mdm2, Double Protein, Hdm2;
Ec: 6.3.2.-
Engineered: Yes
Synthetic: Yes
Other_details: Mdm2 Sequence Occurs Naturally In Humans.

Molecule: D-Peptide Inhibitor
Chain: B, D, F
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide, D-Enantiomer Of Phage-Sel Peptide
symmetry Space Group: C 2 2 21
R_factor 0.209 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
68.976 213.478 45.536 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand CL, DAL, DAR, DGL, DLE, DLY, DSG, DTR, DTY, GOL, SO4 enzyme Ligase E.C.6.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, E


Primary referenceA left-handed solution to peptide inhibition of the p53-MDM2 interaction., Liu M, Pazgier M, Li C, Yuan W, Li C, Lu W, Angew Chem Int Ed Engl. 2010 May 10;49(21):3649-52. PMID:20449836
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (3lnj.pdb1.gz) 34 Kb
  • Biological Unit Coordinates (3lnj.pdb2.gz) 33 Kb
  • LPC: Ligand-Protein Contacts for 3LNJ
  • CSU: Contacts of Structural Units for 3LNJ
  • Structure Factors (327 Kb)
  • Retrieve 3LNJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LNJ from S2C, [Save to disk]
  • Re-refined 3lnj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3LNJ 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 3LNJ
  • 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
  • 3D motif for 3LNJ, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3lnj_F] [3lnj_E] [3lnj] [3lnj_A] [3lnj_B] [3lnj_D] [3lnj_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3LNJ
  • Community annotation for 3LNJ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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