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 Diffractionresolution 2.70 Å
ligand GTP, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
P


Primary referenceStructural 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] (115 Kb) [Save to disk]
  • Biological Unit Coordinates (3ud4.pdb1.gz) 110 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
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3UD4, from MSDmotif at EBI
  • Fold representative 3ud4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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
  • Alignments of the sequence of 3UD4 with the sequences similar proteins can be viewed for 3UD4's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3UD4
  • Community annotation for 3UD4 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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