5Z3A

Glycosidase Wild Type


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.401 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.116 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Glycosidase Wild Type

Tanaka, Y.Chen, M.Tagami, T.Yao, M.Kimura, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycoside hydrolase 15-related protein
A
405Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)Mutation(s): 0 
EC: 3.2.1.205
Find proteins for D2PPM8 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399))
Go to UniProtKB:  D2PPM8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.401 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.116 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 104.743α = 90.00
b = 104.743β = 90.00
c = 89.486γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Platform for Drug Discovery, Informatics, and Structural Life Science(PDIS)Japan--

Revision History 

  • Version 1.0: 2019-05-15
    Type: Initial release