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 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure of SucA with glycolaldehyde-1-13C from Vibrio vulnificus at 2.28 Angstroms resolution.

Seo, P.W.Kim, J.S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Oxoglutarate dehydrogenase (Succinyl-transferring), E1 componentA, B, C, D886Vibrio vulnificus CMCP6Mutation(s): 0 
Gene Names: sucAVV1_0157
EC: 1.2.4.2
Find proteins for A0A3Q0L1E1 (Vibrio vulnificus (strain CMCP6))
Explore A0A3Q0L1E1 
Go to UniProtKB:  A0A3Q0L1E1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

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A, B, C, D
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
P6G
Query on P6G

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A, B, C, D
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
DW3
Query on DW3

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A, B, C, D
2-oxidanylethanal
C2 H4 O2
WGCNASOHLSPBMP-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-07-31 
  • Released Date: 2020-08-05 
  • Deposition Author(s): Seo, P.W., Kim, J.S.

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

Revision History 

  • Version 1.0: 2020-08-05
    Type: Initial release