3UD4	Signaling Protein Rna	date	Oct 27, 2011
title	The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
authors	K.D.Smith, S.A.Strobel
compound		source
Molecule: U1 Small Nuclear Ribonucleoprotein A Chain: P Fragment: Rna Binding Domain, Unp Residues 1-98 Synonym: U1 Snrnp A, U1-A, U1a Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Snrpa Expression_system: Escherichia Coli Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet11
Molecule: Rna (92-Mer) Chain: R Engineered: Yes Other_details: C-Di-Gmp-I Riboswitch		Synthetic: Yes Other_details: In Vitro Transcribed Rna Transcript
Molecule: Rna (5'-R(Gpa)-3') Chain: B Engineered: Yes Other_details: Gpa		Synthetic: Yes
symmetry	Space Group: P 1 21 1	R_factor 0.222 R_Free 0.290
crystal cell	length a length b length c angle alpha angle beta angle gamma 49.612 45.116 76.049 90.00 96.05 90.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand	GTP, MG	enzyme
Gene Ontology	Chain Function Process Component P
Primary reference	Structural and biochemical characterization of linear dinucleotide analogs bound to the c-di-GMP-I aptamer., Smith KD, Lipchock SV, Strobel SA, Biochemistry. 2011 Dec 8. PMID:22148472

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (113 Kb) [Save to disk] Biological Unit Coordinates (3ud4.pdb1.gz) 107 Kb LPC: Ligand-Protein Contacts for 3UD4 CSU: Contacts of Structural Units for 3UD4 Structure Factors (139 Kb) Retrieve 3UD4 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3UD4 from S2C, [Save to disk] Re-refined 3ud4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3UD4 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 3UD4

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 3D motif for 3UD4, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ud4_R] [3ud4_B] [3ud4_P] [3ud4] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3UD4: [RRM ] by SMART

Other resources with information on 3UD4

Community annotation for 3UD4 at PDBWiki (http://pdbwiki.org)

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