1D5N Oxidoreductase date Oct 08, 1999
title Crystal Structure Of E. Coli Mnsod At 100k
authors G.E.O.Borgstahl, M.Pokross, R.Chehab, A.Sekher, E.H.Snell
compound source
Molecule: Protein (Manganese Superoxide Dismutase)
Chain: A, B, C, D
Ec: 1.15.1.1
Organism_scientific: Escherichia Coli
Organism_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.194 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.110 107.300 179.110 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.55 Å
ligand MN enzyme Oxidoreductase E.C.1.15.1.1 BRENDA
related structures by homologous chain: 1I0H, 1Y67
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceCryo-trapping the six-coordinate, distorted-octahedral active site of manganese superoxide dismutase., Borgstahl GE, Pokross M, Chehab R, Sekher A, Snell EH, J Mol Biol 2000 Mar 3;296(4):951-9. PMID:10686094
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (157 Kb) [Save to disk]
  • Biological Unit Coordinates (1d5n.pdb1.gz) 78 Kb
  • Biological Unit Coordinates (1d5n.pdb2.gz) 78 Kb
  • LPC: Ligand-Protein Contacts for 1D5N
  • CSU: Contacts of Structural Units for 1D5N
  • Likely Quarternary Molecular Structure file(s) for 1D5N
  • Structure Factors (1043 Kb)
  • Retrieve 1D5N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D5N from S2C, [Save to disk]
  • Re-refined 1d5n structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1D5N 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 1D5N
  • 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 1D5N, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d5na1, region A:1-90 [Jmol] [rasmolscript] [script source]
        - Domain d1d5na2, region A:91-205 [Jmol] [rasmolscript] [script source]
        - Domain d1d5nb1, region B:1-90 [Jmol] [rasmolscript] [script source]
        - Domain d1d5nb2, region B:91-205 [Jmol] [rasmolscript] [script source]
        - Domain d1d5nc1, region C:1-90 [Jmol] [rasmolscript] [script source]
        - Domain d1d5nc2, region C:91-205 [Jmol] [rasmolscript] [script source]
        - Domain d1d5nd1, region D:1-90 [Jmol] [rasmolscript] [script source]
        - Domain d1d5nd2, region D:91-205 [Jmol] [rasmolscript] [script source]
  • Fold representative 1d5n from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1d5n_D] [1d5n_C] [1d5n] [1d5n_A] [1d5n_B]
  • SWISS-PROT database: [P00448]
  • Domain organization of [SODM_ECOLI] by SWISSPFAM
  • Other resources with information on 1D5N
  • Community annotation for 1D5N 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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