6JWF

Holo form of Pyranose Dehydrogenase PQQ domain from Coprinopsis cinerea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The holo form structure of the catalytic domain of a eukaryotic PQQ-dependent dehydrogenase

Takeda, K.Ishida, T.Yoshida, M.Samejima, M.Ohno, H.Igarashi, K.Nakamura, N.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Extracellular PQQ-dependent sugar dehydrogenase
A, B
410Coprinopsis cinereaMutation(s): 0 
Gene Names: CcSDH
Find proteins for A0A0A8IDB7 (Coprinopsis cinerea)
Go to UniProtKB:  A0A0A8IDB7
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PQQ
Query on PQQ

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Download CCD File 
A, B
PYRROLOQUINOLINE QUINONE
C14 H6 N2 O8
MMXZSJMASHPLLR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 85.330α = 90.00
b = 95.638β = 90.00
c = 106.204γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan17K17703

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release