5GMV Protein Binding date Jul 17, 2016
title Lc3b-Fundc1 Complex
authors M.Lv, C.Wang, F.Li
compound source
Molecule: Microtubule-Associated Proteins 1a1b Light Chain
Chain: B, A
Synonym: Autophagy-Related Protein Lc3 B,Autophagy-Related Like Modifier Lc3 B,Map1 Light Chain 3-Like Protein 2,Map1a Light Chain 3 B,Map1amap1b Lc3 B,Microtubule-Associated Pr Light Chain 3 Beta;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Map1lc3b, Map1alc3
Expression_system: Escherichia Coli K-12
Expression_system_taxid: 83333
Expression_system_strain: K-12
Expression_system_vector_type: Plasmid

Molecule: Peptide From Fun14 Domain-Containing Protein 1
Chain: D, C
Synonym: Fundc1 Peptide
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.206 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.537 86.850 40.537 90.00 110.86 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand SEP enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural insights into the recognition of phosphorylated FUNDC1 by LC3B in mitophagy., Lv M, Wang C, Li F, Peng J, Wen B, Gong Q, Shi Y, Tang Y, Protein Cell. 2017 Jan;8(1):25-38. doi: 10.1007/s13238-016-0328-8. Epub 2016 Oct , 18. PMID:27757847
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (5gmv.pdb1.gz) 23 Kb
  • Biological Unit Coordinates (5gmv.pdb2.gz) 23 Kb
  • LPC: Ligand-Protein Contacts for 5GMV
  • CSU: Contacts of Structural Units for 5GMV
  • Structure Factors (258 Kb)
  • Retrieve 5GMV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GMV from S2C, [Save to disk]
  • Re-refined 5gmv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5GMV 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 5GMV
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5gmv_D] [5gmv_A] [5gmv_B] [5gmv_C] [5gmv]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5GMV
  • Community annotation for 5GMV at PDBWiki (http://pdbwiki.org)

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