3DX1

Golgi alpha-Mannosidase II in complex with Mannostatin analog (1S,2S,3R,4R)-4-aminocyclopentane-1,2,3-triol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.127 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-mannosidase 21,045Drosophila melanogasterMutation(s): 0 
Gene Names: alpha-Man-IIGmIICG18802
EC: 3.2.1.114
UniProt
Find proteins for Q24451 (Drosophila melanogaster)
Explore Q24451 
Go to UniProtKB:  Q24451
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ24451
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
YHO
Query on YHO

Download Ideal Coordinates CCD File 
F [auth A](1S,2S,3R,4R)-4-aminocyclopentane-1,2,3-triol
C5 H11 N O3
UUKWSEIZIMUXPU-LECHCGJUSA-N
MRD
Query on MRD

Download Ideal Coordinates CCD File 
E [auth A](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
YHO PDBBind:  3DX1 Ki: 2.65e+5 (nM) from 1 assay(s)
BindingDB:  3DX1 Ki: 2.65e+5 (nM) from 1 assay(s)
Binding MOAD:  3DX1 Ki: 2.65e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.127 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.917α = 90
b = 109.539β = 90
c = 138.689γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
SHELXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
CNSphasing
DENZOdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary