8PA2

Crystal structure of alcohol dehydrogenase/ketoreductase variant from Thermus thermophilus apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.215 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NADClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

Crystal structure of alcohol dehydrogenase/ketoreductase variant from Thermus thermophilus apo form

Delgado-Arciniega, E.Bodescu, V.Rozeboom, H.J.Janssen, D.B.Wijma, H.J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxidoreductase, short-chain dehydrogenase/reductase family
A, B, C, D
264Thermus thermophilus HB8Mutation(s): 9 
Gene Names: TTHA0369
UniProt
Find proteins for Q5SLC4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLC4 
Go to UniProtKB:  Q5SLC4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SLC4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
J [auth C],
L [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
B3P
Query on B3P

Download Ideal Coordinates CCD File 
F [auth A]2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth B],
I [auth C],
K [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.215 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.981α = 90
b = 92.937β = 107.87
c = 79.601γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NADClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release