1O7D

THE STRUCTURE OF THE BOVINE LYSOSOMAL A-MANNOSIDASE SUGGESTS A NOVEL MECHANISM FOR LOW PH ACTIVATION

Structural Biology Knowledgebase: 1O7D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.257

Literature

Macromolecules
Sequence Display for 1O7D

Classification: HYDROLASE

Total Structure Weight: 111487.91

Macromolecule Entities
Molecule Chains Length Organism Details
LYSOSOMAL ALPHA-MANNOSIDASE A 298 Bos taurus EC#: 3.2.1.24 IUBMB
Fragment: ALPHA-MANNOSIDASE A PEPTIDE, RESIDUES 51-347
Mutation: R175G
Details: GLYCOSYLATED
Gene Name(s): MAN2B1 Gene View MANB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
LYSOSOMAL ALPHA-MANNOSIDASE B 84 Bos taurus EC#: 3.2.1.24 IUBMB
Fragment: ALPHA-MANNOSIDASE B PEPTIDE, RESIDUES 348-431
Mutation: S356P
Details: GLYCOSYLATED
Gene Name(s): MAN2B1 Gene View MANB
LYSOSOMAL ALPHA-MANNOSIDASE C 159 Bos taurus EC#: 3.2.1.24 IUBMB
Fragment: ALPHA-MANNOSIDASE C PEPTIDE, RESIDUES 432-590
Details: GLYCOSYLATED
Gene Name(s): MAN2B1 Gene View MANB
LYSOSOMAL ALPHA-MANNOSIDASE D 282 Bos taurus EC#: 3.2.1.24 IUBMB
Fragment: ALPHA-MANNOSIDASE D PEPTIDE, RESIDUES 592-873
Details: GLYCOSYLATED
Gene Name(s): MAN2B1 Gene View MANB
LYSOSOMAL ALPHA-MANNOSIDASE E 126 Bos taurus EC#: 3.2.1.24 IUBMB
Fragment: ALPHA-MANNOSIDASE E PEPTIDE, RESIDUES 874-999
Details: GLYCOSYLATED
Gene Name(s): MAN2B1 Gene View MANB

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A, C, D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NDG
Query on NDG

C, D 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

C BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

C ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRS
Query on TRS

A 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, E SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.257
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 117.88 α = 90.00
b = 117.88 β = 90.00
c = 582.04 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-10-30
  • Released Date: 2003-03-20
  • Deposition author(s): Heikinheimo, P., Helland, R., Leiros, H.S., Leiros, I., Karlsen, S., Evjen, G., Ravelli, R., Schoehn, G., Ruigrok, R., Tollersrud, O.-K., Mcsweeney, S., Hough, E.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4