5Y5R

Crystal structure of a novel Pyrethroid Hydrolase PytH with BIF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.276 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structure and Catalytic Mechanism of a Novel Pyrethroid Hydrolase from Sphingobium faniae JZ-2

Xu, D.Q.Ran, T.T.He, J.Wang, W.W.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyrethroid hydrolase
A, B, C, D, E, F
A, B, C, D, E, F
288Sphingobium faniaeMutation(s): 0 
Gene Names: pytH
UniProt
Find proteins for D0VUS3 (Sphingobium faniae)
Explore D0VUS3 
Go to UniProtKB:  D0VUS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VUS3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8NL
Query on 8NL

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
(2-methyl-3-phenyl-phenyl)methyl (1~{S})-3-[(~{E})-2-chloranyl-3,3,3-tris(fluoranyl)prop-1-enyl]-2,2-dimethyl-cyclopropane-1-carboxylate
C23 H22 Cl F3 O2
OMFRMAHOUUJSGP-AZUAARDMSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.276 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.857α = 90
b = 168.857β = 90
c = 123.864γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release