6R3L

Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with the covalent adduct formed between prFMN cofactor and cinnamic acid following decarboxylation (Int3)

  • Classification: LYASE
  • Organism(s): Aspergillus niger
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-03-20 Released: 2019-08-28 
  • Deposition Author(s): Bailey, S.S., Leys, D.
  • Funding Organization(s): European Research Council, Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Atomic description of an enzyme reaction dependent on reversible 1,3-dipolar cycloaddition

Bailey, S.S., Payne, K.A.P., Saaret, A., Marshall, S.A., Gostimskaya, I., Kosov, I., Fisher, K., Hay, S., Leys, D.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferulic acid decarboxylase 1508Aspergillus nigerMutation(s): 0 
Gene Names: fdc1, An03g06590
EC: 4.1.1.102
UniProt
Find proteins for A2QHE5 (Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513))
Explore A2QHE5 
Go to UniProtKB:  A2QHE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2QHE5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JSH
Query on JSH
Download Ideal Coordinates CCD File 
E [auth A]prFMN cofactor and cinnamic acid adduct
C30 H37 N4 O9 P
WCKFFLZBWSLRDK-BEFVXGCNSA-N
BYN
Query on BYN
Download Ideal Coordinates CCD File 
F [auth A]hydroxylated prenyl-FMN
C22 H31 N4 O10 P
BDNVCRCOZIAGID-LWGWVAHUSA-N
SYN
Query on SYN
Download Ideal Coordinates CCD File 
G [auth A]ethenylbenzene
C8 H8
PPBRXRYQALVLMV-UHFFFAOYSA-N
MN
Query on MN
Download Ideal Coordinates CCD File 
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
K
Query on K
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.923α = 90
b = 64.219β = 90
c = 87.773γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdompreFAB 695013
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K017802

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description