6KMA

Crystal structure of SucA with glycolaldehyde-1-13C from Vibrio vulnificus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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

Understanding the molecular properties of the E1 subunit (SucA) of alpha-ketoglutarate dehydrogenase complex from Vibrio vulnificus for the enantioselective ligation of acetaldehydes into (R)-acetoin.

Seo, P.W.Jo, H.J.Hwang, I.Y.Jeong, H.Y.Kim, J.H.Kim, J.W.Lee, E.Y.Park, J.B.Kim, J.S.

(2020) Catal Sci Technol 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component
A, B, C, D
886Vibrio vulnificus CMCP6Mutation(s): 0 
Gene Names: sucAVV1_0157
EC: 1.2.4.2
UniProt
Find proteins for A0A3Q0L1E1 (Vibrio vulnificus (strain CMCP6))
Explore A0A3Q0L1E1 
Go to UniProtKB:  A0A3Q0L1E1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3Q0L1E1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP (Subject of Investigation/LOI)
Query on TPP

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B],
S [auth C],
Y [auth D]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
P6G
Query on P6G

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E [auth A],
L [auth B],
P [auth C],
W [auth D]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
DW3 (Subject of Investigation/LOI)
Query on DW3

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth B]
O [auth B]
T [auth C]
I [auth A],
J [auth A],
K [auth B],
O [auth B],
T [auth C],
U [auth C],
V [auth D],
Z [auth D]
2-oxidanylethanal
C2 H4 O2
WGCNASOHLSPBMP-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
Q [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B],
R [auth C],
X [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.82α = 79.51
b = 84.559β = 88.47
c = 145.218γ = 89.92
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2021-02-24
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description