5Z3D

Glycosidase F290Y


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.114 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Glycosidase F290Y

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycoside hydrolase 15-related proteinA405Kribbella flavida DSM 17836Mutation(s): 1 
Gene Names: Kfla_1896
EC: 3.2.1.205
UniProt
Find proteins for D2PPM8 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399))
Explore D2PPM8 
Go to UniProtKB:  D2PPM8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
D [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
AL-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.114 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.725α = 90
b = 104.725β = 90
c = 89.319γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

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