5DPR Protein Binding date Sep 14, 2015
title Crystal Structure Of Plekhm1 Lir-Fused Human Lc3a_2-121
authors A.C.Ravichandran, H.Suzuki, R.C.J.Dobson
compound source
Molecule: Pleckstrin Homology Domain-Containing Family M Me Microtubule-Associated Proteins 1a1b Light Chain 3a;
Chain: A, B, C, D
Fragment: Unp Q9y4g2 Residues 627-638, Unp Q9h492 Residues Q9y4g2 Residues 627-638, Unp Q9h492 Residues 2-121;
Synonym: Ph Domain-Containing Family M Member 1,162 Kda Ada Protein,Ap162,Autophagy-Related Protein Lc3 A,Autophagy-Rel Ubiquitin-Like Modifier Lc3 A,Map1 Light Chain 3-Like Prote Map1amap1b Light Chain 3 A,Map1amap1b Lc3 A,Microtubule-A Protein 1 Light Chain 3 Alpha;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Plekhm1, Kiaa0356, Map1lc3a
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30
symmetry Space Group: P 1 21 1
R_factor 0.218 R_Free 0.261
length a length b length c angle alpha angle beta angle gamma
62.700 63.082 84.924 90.00 100.94 90.00
method X-Ray Diffractionresolution 2.50 Å
A, D, C, B

Primary referenceStructural and functional analysis of the GABARAP interaction motif (GIM)., Rogov VV, Stolz A, Ravichandran AC, Rios-Szwed DO, Suzuki H, Kniss A, Lohr F, Wakatsuki S, Dotsch V, Dikic I, Dobson RC, McEwan DG, EMBO Rep. 2017 Aug;18(8):1382-1396. doi: 10.15252/embr.201643587. Epub 2017 Jun, 27. PMID:28655748
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (260 Kb) [Save to disk]
  • Biological Unit Coordinates (5dpr.pdb1.gz) 63 Kb
  • Biological Unit Coordinates (5dpr.pdb2.gz) 66 Kb
  • Biological Unit Coordinates (5dpr.pdb3.gz) 65 Kb
  • Biological Unit Coordinates (5dpr.pdb4.gz) 64 Kb
  • CSU: Contacts of Structural Units for 5DPR
  • Structure Factors (398 Kb)
  • Retrieve 5DPR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DPR from S2C, [Save to disk]
  • Re-refined 5dpr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DPR 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 5DPR
  • 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 5dpr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dpr_B] [5dpr_C] [5dpr_A] [5dpr] [5dpr_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5DPR
  • Community annotation for 5DPR at PDBWiki (http://pdbwiki.org)

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