1M5O Translation Rna date Jul 09, 2002
title Transition State Stabilization By A Catalytic Rna
authors P.B.Rupert, A.P.Massey, S.T.Sigurdsson, A.R.Ferre-D'Amare
compound source
Molecule: Rna Substrate
Chain: A, D
Engineered: Yes
Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Satellite Tobacco Ringspot Virus;

Molecule: Rna Hairpin Ribozyme
Chain: B, E
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Satellite Tobacco Ringspot Virus;

Molecule: U1 Small Nuclear Ribonucleoprotein A
Chain: C, F
Fragment: U1a Rna Binding Domain
Synonym: U1 Snrnp A Protein; U1 Snrnp-Specific Protein A
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpa
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
symmetry Space Group: C 1 2 1
R_factor 0.229 R_Free 0.264
crystal
cell
length a length b length c angle alpha angle beta angle gamma
259.380 44.220 102.500 90.00 106.30 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand AVC, CA enzyme
related structures by homologous chain: 1SJ3, 1URN
Primary referenceTransition state stabilization by a catalytic RNA., Rupert PB, Massey AP, Sigurdsson ST, Ferre-D'Amare AR, Science 2002 Nov 15;298(5597):1421-4. Epub 2002 Oct 10. PMID:12376595
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (139 Kb) [Save to disk]
  • Biological Unit Coordinates (1m5o.pdb1.gz) 67 Kb
  • Biological Unit Coordinates (1m5o.pdb2.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 1M5O
  • CSU: Contacts of Structural Units for 1M5O
  • Likely Quarternary Molecular Structure file(s) for 1M5O
  • Structure Factors (648 Kb)
  • Retrieve 1M5O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1M5O from S2C, [Save to disk]
  • Re-refined 1m5o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1M5O 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 1M5O
  • 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 1M5O, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m5oc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1m5of_, region F [Jmol] [rasmolscript] [script source]
  • Fold representative 1m5o from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1m5o_E] [1m5o_C] [1m5o_D] [1m5o] [1m5o_A] [1m5o_B] [1m5o_F]
  • SWISS-PROT database: [P09012]
  • Domain organization of [SNRPA_HUMAN] by SWISSPFAM
  • Domain found in 1M5O: [RRM ] by SMART
  • Other resources with information on 1M5O
  • Community annotation for 1M5O at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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