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
crystal cell	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 Diffraction	resolution	2.50 Å
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Structural 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] (254 Kb) [Save to disk] Biological Unit Coordinates (5dpr.pdb1.gz) 62 Kb Biological Unit Coordinates (5dpr.pdb2.gz) 64 Kb Biological Unit Coordinates (5dpr.pdb3.gz) 63 Kb Biological Unit Coordinates (5dpr.pdb4.gz) 62 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

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: [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)

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---