5OEX

Complex with iodine ion for thiocyanate dehydrogenase from Thioalkalivibrio paradoxus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery and characterization of a novel copper containing enzyme - THIOCYANATE DEHYDROGENASE.

Tikhonova, T.V.Sorokin, D.I.Tsallagov, S.I.Polyakov, K.M.Trofimov, A.A.Shabalin, I.G.Khrenova, M.G.Muyser, G.Rakitina, T.V.Popov, V.O.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THIOCYANATE DEHYDROGENASE
A, B, C, D
467Thioalkalivibrio paradoxus ARh 1Mutation(s): 0 
Gene Names: THITH_13335
UniProt
Find proteins for W0DP94 (Thioalkalivibrio paradoxus ARh 1)
Explore W0DP94 
Go to UniProtKB:  W0DP94
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW0DP94
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P4G
Query on P4G

Download Ideal Coordinates CCD File 
I [auth A]1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
C8 H18 O3
RRQYJINTUHWNHW-UHFFFAOYSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
DA [auth D]
EA [auth D]
FA [auth D]
J [auth A]
K [auth A]
DA [auth D],
EA [auth D],
FA [auth D],
J [auth A],
K [auth A],
L [auth A],
X [auth C],
Y [auth C]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL
Query on GOL

Download Ideal Coordinates CCD File 
S [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
E [auth A]
F [auth A]
AA [auth D],
BA [auth D],
CA [auth D],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
Z [auth D]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
P [auth B],
Q [auth B],
R [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.82α = 90
b = 159.45β = 97.77
c = 91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FondationRussian Federation15-14-00063

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description