5X6V	Protein Binding	date	Feb 23, 2017
title	Crystal Structure Of Human Heteroheptameric 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
Molecule: Ras-Related Gtp-Binding Protein A Chain: F Fragment: Unp Residues 183-313 Synonym: Raga,Adenovirus E3 14.7 Kda-Interacting Protein 1, Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Rraga Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Ras-Related Gtp-Binding Protein C Chain: G Fragment: Unp Residues 238-375 Synonym: Ragc,Gtpase-Interacting Protein 2,Tib929 Engineered: Yes		Organism_scientific: Mus Musculus Organism_common: Mouse Organism_taxid: 10090 Gene: Rragc Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 21 21 21	R_factor 0.193 R_Free 0.243
crystal cell	length a length b length c angle alpha angle beta angle gamma 74.099 93.476 125.452 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.02 Å
ligand	ACT, NA	enzyme
Gene Ontology	Chain Function Process Component A B C D E F, G
Primary reference	Structural 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] (264 Kb) [Save to disk] Biological Unit Coordinates (5x6v.pdb1.gz) 257 Kb LPC: Ligand-Protein Contacts for 5X6V CSU: Contacts of Structural Units for 5X6V Structure Factors (2433 Kb) Retrieve 5X6V in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5X6V from S2C, [Save to disk]

View 5X6V 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 5X6V

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5x6v_D] [5x6v_G] [5x6v_E] [5x6v_C] [5x6v_F] [5x6v_B] [5x6v_A] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 5X6V

Community annotation for 5X6V 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

---