5DTC	Protein Binding	date	Sep 17, 2015
title	Ubl Structure
authors	E.M.Romes, R.E.Stanley
compound		source
Molecule: Ribosome Biogenesis Protein Ytm1 Chain: A, B Fragment: Unp Residues 5-92 Engineered: Yes		Organism_scientific: Saccharomyces Cerevisiae Organism_taxid: 1294333 Strain: Yjm1133 Gene: Ytm1, H781_yjm1133o00421 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3)Star Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgst2
symmetry	Space Group: P 1	R_factor 0.175 R_Free 0.232
crystal cell	length a length b length c angle alpha angle beta angle gamma 35.298 37.738 41.134 82.54 64.31 69.62
method	X-Ray Diffraction	resolution	1.70 Å
Gene	H781
Primary reference	The Crystal Structure of the Ubiquitin-Like Domain of Ribosome Assembly Factor Ytm1 and Characterization of its Interaction with the AAA-ATPase Midasin., Romes EM, Sobhany M, Stanley RE, J Biol Chem. 2015 Nov 24. pii: jbc.M115.693259. PMID:26601951

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk] Biological Unit Coordinates (5dtc.pdb1.gz) 31 Kb Biological Unit Coordinates (5dtc.pdb2.gz) 31 Kb CSU: Contacts of Structural Units for 5DTC Structure Factors (315 Kb) Retrieve 5DTC in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5DTC from S2C, [Save to disk] Re-refined 5dtc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5DTC 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 5DTC

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: [5dtc_B] [5dtc] [5dtc_A] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 5DTC

Community annotation for 5DTC at PDBWiki (http://pdbwiki.org)

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