8TWN

Crystal structure of nitrile synthase AetD with substrate bound

  • 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: 2.08 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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
AetD260Aetokthonos 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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
67I (Subject of Investigation/LOI)
Query on 67I
Download Ideal Coordinates CCD File 
B [auth A](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 
C [auth A]D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.554α = 90
b = 101.554β = 90
c = 129.094γ = 120
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