1M5K Translation Rna date Jul 09, 2002
title Crystal Structure Of A Hairpin Ribozyme In The Catalytically Conformation
authors P.B.Rupert, A.R.Ferre-D'Amare
compound source
Molecule: Rna Inhibitor Substrate
Chain: A, D
Engineered: Yes
Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Satellite Ringspot Virus;

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

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

Molecule: Protein (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 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
256.300 44.100 102.400 90.00 109.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand A2M, CA, CL, GTP, IU enzyme
note 1M5K supersedes 1HP6
related structures by homologous chain: 1M5V, 1VC7
Primary referenceCrystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis., Rupert PB, Ferre-D'Amare AR, Nature 2001 Apr 12;410(6830):780-6. PMID:11298439
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (137 Kb) [Save to disk]
  • Biological Unit Coordinates (1m5k.pdb1.gz) 67 Kb
  • Biological Unit Coordinates (1m5k.pdb2.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 1M5K
  • CSU: Contacts of Structural Units for 1M5K
  • Likely Quarternary Molecular Structure file(s) for 1M5K
  • Structure Factors (462 Kb)
  • Retrieve 1M5K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1M5K from S2C, [Save to disk]
  • Re-refined 1m5k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1M5K 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 1M5K
  • 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 1M5K, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m5kc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1m5kf_, region F [Jmol] [rasmolscript] [script source]
  • Fold representative 1m5k 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: [1m5k] [1m5k_A] [1m5k_E] [1m5k_D] [1m5k_C] [1m5k_B] [1m5k_F]
  • SWISS-PROT database: [P09012]
  • Domain organization of [SNRPA_HUMAN] by SWISSPFAM
  • Domain found in 1M5K: [RRM ] by SMART
  • Alignments of the sequence of 1M5K with the sequences similar proteins can be viewed for 1M5K's classification [SNRPA_HUMAN] 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 [SNRPA_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1M5K
  • Community annotation for 1M5K 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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