5X6U Protein Binding date Feb 23, 2017
title Crystal Structure Of Human Heteropentameric Complex
authors R.Yonehara, S.Nada, T.Nakai, M.Nakai, A.Kitamura, A.Ogawa, H.Nakat K.I.Nakayama, S.Li, D.M.Standley, E.Yamashita, A.Nakagawa, M.Oka
compound source
Molecule: Ragulator Complex Protein Lamtor3
Chain: A
Synonym: Late Endosomallysosomal Adaptor And Mapk And Mtor 3,Mek-Binding Partner 1,Mp1,Mitogen-Activated Protein Kinas 1-Interacting Protein 1,Mitogen-Activated Protein Kinase Sc Protein 1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lamtor3, Map2k1ip1, Mapksp1, Pro2783
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ragulator Complex Protein Lamtor2
Chain: B
Synonym: Endosomal Adaptor Protein P14,Late Endosomallysos Interacting Protein,Late Endosomallysosomal Adaptor And Ma Mtor Activator 2,Mitogen-Activated Protein-Binding Protein- Interacting Protein,Mapbp-Interacting Protein,Roadblock Dom Containing Protein 3;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lamtor2, Mapbpip, Robld3, Hspc003
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ragulator Complex Protein Lamtor5
Chain: C
Synonym: Hepatitis B Virus X-Interacting Protein,Hbx-Intera Protein,Late Endosomallysosomal Adaptor And Mapk And Mtor 5;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lamtor5, Hbxip, Xip
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ragulator Complex Protein Lamtor4
Chain: D
Synonym: Late Endosomallysosomal Adaptor And Mapk And Mtor 4;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lamtor4, C7orf59
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ragulator Complex Protein Lamtor1
Chain: E
Fragment: Unp Residues 42-161
Synonym: Late Endosomallysosomal Adaptor And Mapk And Mtor 1,Lipid Raft Adaptor Protein P18,Protein Associated With Dr Endosomes,P27kip1-Releasing Factor From Rhoa,P27rf-Rho;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lamtor1, C11orf59, Pdro, Pp7157
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 41 2 2
R_factor 0.186 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
133.038 133.038 75.147 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


Primary referenceStructural basis for the assembly of the Ragulator-Rag GTPase complex., Yonehara R, Nada S, Nakai T, Nakai M, Kitamura A, Ogawa A, Nakatsumi H, Nakayama KI, Li S, Standley DM, Yamashita E, Nakagawa A, Okada M, Nat Commun. 2017 Nov 20;8(1):1625. doi: 10.1038/s41467-017-01762-3. PMID:29158492
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (170 Kb) [Save to disk]
  • Biological Unit Coordinates (5x6u.pdb1.gz) 164 Kb
  • CSU: Contacts of Structural Units for 5X6U
  • Structure Factors (449 Kb)
  • Retrieve 5X6U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5X6U from S2C, [Save to disk]
  • View 5X6U 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 5X6U
  • 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 5x6u from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5x6u_A] [5x6u_B] [5x6u_D] [5x6u_C] [5x6u_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5X6U
  • Community annotation for 5X6U at PDBWiki (http://pdbwiki.org)

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