1B2M Hydrolase Rna date Nov 27, 1998
title Three-Dimensional Structure Of Ribonulcease T1 Complexed Wit Isosteric Phosphonate Analogue Of Gpu: Alternate Substrate Modes And Catalysis.
authors R.K.Arni, L.Watanabe, R.J.Ward, R.J.Kreitman, K.Kumar, F.G.Walz J
compound source
Molecule: 5'-R(Gp(U34))-3'
Chain: C, D, E
Engineered: Yes
Synthetic: Yes

Molecule: Ribonuclease T1
Chain: A, B
Ec: 3.1.27.3
Mutation: Yes
Other_details: Rnase T1 Complexed With 5'-R(Gp(Ch2)U)-3

Organism_scientific: Aspergillus Oryzae
Organism_taxid: 5062
symmetry Space Group: P 21 21 21
R_factor 0.187 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.910 90.290 33.980 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand U34 enzyme Hydrolase E.C.3.1.27.3 BRENDA
related structures by homologous chain: 1FYS, 4HOH
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • endonuclease activity
  • endoribonuclease activity
  • ribonuclease activity


  • Primary referenceThree-dimensional structure of ribonuclease T1 complexed with an isosteric phosphonate substrate analogue of GpU: alternate substrate binding modes and catalysis., Arni RK, Watanabe L, Ward RJ, Kreitman RJ, Kumar K, Walz FG Jr, Biochemistry. 1999 Feb 23;38(8):2452-61. PMID:10029539
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (41 Kb) [Save to disk]
  • Biological Unit Coordinates (1b2m.pdb1.gz) 19 Kb
  • Biological Unit Coordinates (1b2m.pdb2.gz) 20 Kb
  • LPC: Ligand-Protein Contacts for 1B2M
  • CSU: Contacts of Structural Units for 1B2M
  • Likely Quarternary Molecular Structure file(s) for 1B2M
  • Retrieve 1B2M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1B2M from S2C, [Save to disk]
  • View 1B2M 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 1B2M
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1B2M, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1b2ma_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1b2mb_, region B [Jmol] [rasmolscript] [script source]
  • 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: [1b2m_C] [1b2m_A] [1b2m_D] [1b2m_E] [1b2m_B] [1b2m]
  • SWISS-PROT database: [P00651]
  • Domain organization of [RNT1_ASPOR] by SWISSPFAM
  • Other resources with information on 1B2M
  • Community annotation for 1B2M 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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