1MH9 Hydrolase date Aug 19, 2002
title Crystal Structure Analysis Of Deoxyribonucleotidase
authors A.Rinaldo-Matthis, C.Rampazzo, P.Reichard, V.Bianchi, P.Nordlund
compound source
Molecule: Deoxyribonucleotidase
Chain: A
Synonym: Mitochondrial 5'(3')-Deoxyribonucleotidase
Ec: 3.1.3.5
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43 21 2
R_factor 0.159 R_Free 0.191
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.965 73.965 105.932 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand MG, PO4 enzyme Hydrolase E.C.3.1.3.5 BRENDA
related structures by homologous chain: 1Q91
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of a human mitochondrial deoxyribonucleotidase., Rinaldo-Matthis A, Rampazzo C, Reichard P, Bianchi V, Nordlund P, Nat Struct Biol 2002 Oct;9(10):779-87. PMID:12352955
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk]
  • Biological Unit Coordinates (1mh9.pdb1.gz) 79 Kb
  • LPC: Ligand-Protein Contacts for 1MH9
  • CSU: Contacts of Structural Units for 1MH9
  • Likely Quarternary Molecular Structure file(s) for 1MH9
  • Structure Factors (280 Kb)
  • Retrieve 1MH9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1MH9 from S2C, [Save to disk]
  • Re-refined 1mh9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1MH9 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 1MH9
  • 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 1MH9, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1mh9a_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1mh9 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: [1mh9_A] [1mh9]
  • SWISS-PROT database: [Q9NPB1]
  • Domain organization of [NT5M_HUMAN] by SWISSPFAM
  • Other resources with information on 1MH9
  • Community annotation for 1MH9 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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