1O7D Hydrolase date Oct 30, 2002
title The Structure Of The Bovine Lysosomal A-Mannosidase Suggests Mechanism For Low Ph Activation
authors P.Heikinheimo, R.Helland, H.S.Leiros, I.Leiros, S.Karlsen, G.Evje R.Ravelli, G.Schoehn, R.Ruigrok, O.K.Tollersrud, S.Mcsweeney, E
compound source
Molecule: Lysosomal Alpha-Mannosidase
Chain: A
Fragment: Alpha-Mannosidase A Peptide, Residues 51-347
Synonym: Laman,Lysosomal Acid Alpha-Mannosidase,Mannosidase Class 2b Member 1,Mannosidase Alpha-B;
Ec: 3.2.1.24
Other_details: Glycosylated
 Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Organ: Kidney

Molecule: Lysosomal Alpha-Mannosidase
Chain: B
Fragment: Alpha-Mannosidase B Peptide, Residues 348-431
Synonym: Laman,Lysosomal Acid Alpha-Mannosidase,Mannosidase Class 2b Member 1,Mannosidase Alpha-B;
Ec: 3.2.1.24
Other_details: Glycosylated
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Organ: Kidney

Molecule: Lysosomal Alpha-Mannosidase
Chain: C
Fragment: Alpha-Mannosidase C Peptide, Residues 432-590
Synonym: Laman,Lysosomal Acid Alpha-Mannosidase,Mannosidase Class 2b Member 1,Mannosidase Alpha-B;
Ec: 3.2.1.24
Other_details: Glycosylated
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Organ: Kidney

Molecule: Lysosomal Alpha-Mannosidase
Chain: D
Fragment: Alpha-Mannosidase D Peptide, Residues 592-873
Synonym: Laman,Lysosomal Acid Alpha-Mannosidase,Mannosidase Class 2b Member 1,Mannosidase Alpha-B;
Ec: 3.2.1.24
Other_details: Glycosylated
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Organ: Kidney

Molecule: Lysosomal Alpha-Mannosidase
Chain: E
Fragment: Alpha-Mannosidase E Peptide, Residues 874-999
Synonym: Laman,Lysosomal Acid Alpha-Mannosidase,Mannosidase Class 2b Member 1,Mannosidase Alpha-B;
Ec: 3.2.1.24
Other_details: Glycosylated
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Organ: Kidney
symmetry Space Group: P 61 2 2
R_factor 0.257 R_Free 0.289
crystal
cell
length a length b length c angle alpha angle beta angle gamma
117.880 117.880 582.040 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand BMA, MAN, NAG, SO4, TRS, ZN enzyme Hydrolase E.C.3.2.1.24 BRENDA
note 1O7D is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


Primary referenceThe structure of bovine lysosomal alpha-mannosidase suggests a novel mechanism for low-pH activation., Heikinheimo P, Helland R, Leiros HK, Leiros I, Karlsen S, Evjen G, Ravelli R, Schoehn G, Ruigrok R, Tollersrud OK, McSweeney S, Hough E, J Mol Biol 2003 Mar 28;327(3):631-44. PMID:12634058
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (145 Kb) [Save to disk]
  • Biological Unit Coordinates (1o7d.pdb1.gz) 137 Kb
  • LPC: Ligand-Protein Contacts for 1O7D
  • CSU: Contacts of Structural Units for 1O7D
  • Likely Quarternary Molecular Structure file(s) for 1O7D
  • Structure Factors (556 Kb)
  • Retrieve 1O7D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1O7D from S2C, [Save to disk]
  • Re-refined 1o7d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1O7D 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 1O7D
  • 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
  • 3D motif for 1O7D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1o7d.3, region A:51-342,B:347-384 [Jmol] [rasmolscript] [script source]
        - Domain d1o7d.1, region B:385-422,C:431-487 [Jmol] [rasmolscript] [script source]
        - Domain d1o7d.2, region C:488-585,D:603-875,E:885-1007 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1o7d_D] [1o7d_C] [1o7d_B] [1o7d] [1o7d_E] [1o7d_A]
  • SWISS-PROT database: [Q29451]
  • Domain organization of [MA2B1_BOVIN] by SWISSPFAM
    • Other resources with information on 1O7D
  • Community annotation for 1O7D 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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