8TWT

Crystal structure of nitrile synthase AetD with substrate bound and cofactor partially assembled

  • Classification: OXIDOREDUCTASE
  • Organism(s): Aetokthonos hydrillicola
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-08-21 Released: 2024-08-28 
  • Deposition Author(s): Ye, N., Drennan, C.L.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 


Literature

Oxidative rearrangement of tryptophan to indole nitrile by a single diiron enzyme

Adak, S., Ye, N., Calderone, L.A., Schafer, R.J.B., Lukowski, A.L., Pandelia, M.-E., Drennan, C.L., Moore, B.S.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AetD
A, B
260Aetokthonos hydrillicolaMutation(s): 0 
Gene Names: aetD
UniProt
Find proteins for A0A861B387 (Aetokthonos hydrillicola Thurmond2011)
Explore A0A861B387 
Go to UniProtKB:  A0A861B387
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A861B387
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
67I (Subject of Investigation/LOI)
Query on 67I
Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]		(2S)-2-azanyl-3-[5,7-bis(bromanyl)-1H-indol-3-yl]propanoic acid
C11 H10 Br2 N2 O2
UURVQGNSCUCIQS-VIFPVBQESA-N
MLT
Query on MLT
Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]		D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
SIN
Query on SIN
Download Ideal Coordinates CCD File 
E [auth A]SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
I [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE
Query on FE
Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
K [auth B]		FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.916α = 90
b = 86.089β = 90
c = 101.779γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM126982
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30-GM124165
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30-GM133894

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-28
    Type: Initial release