7BXQ

2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator L-Threonine binding form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

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

Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase

Motoyama, T.Nakano, S.Hasebe, F.Miyata, R.Kumazawa, S.Miyoshi, N.Ito, S.

(2021) Commun Chem 4: 108-108


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-amino-3-ketobutyrate coenzyme A ligase
A, B
411Cupriavidus necatorMutation(s): 0 
Gene Names: kblH16_B0819
EC: 2.3.1.29
UniProt
Find proteins for Q0K313 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337))
Explore Q0K313 
Go to UniProtKB:  Q0K313
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0K313
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2BK (Subject of Investigation/LOI)
Query on 2BK

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-allothreonine
C12 H19 N2 O8 P
IZWQBQLGLAKRMN-XVKPBYJWSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.708α = 90
b = 101.657β = 112.99
c = 69.854γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18K14391
Japan Society for the Promotion of Science (JSPS)Japan19J23697

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-21
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description