4WPD | pdb_00004wpd

X-ray Crystal Structure of CYP119 complexed with 4-(4-flourophenyl)-1H-imidazole

• PDB DOI: https://doi.org/10.2210/pdb4WPD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sulfolobus acidocaldarius DSM 639
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-10-17 Released: 2015-02-18 
• Deposition Author(s): Madrona, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Literature

TWO DIMENTIONAL NMR AND X-RAY ANALYSIS OF CYP119 LIGAND DEPENDENT CONFORMATIONAL DYNAMICS

Basudhar, D., Madrona, Y., Kandel, S., Lampe, J.N., Ortiz de Montellano, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 87.41 kDa 
• Atom Count: 6,972 
• Modeled Residue Count: 734 
• Deposited Residue Count: 736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 119	A, B	368	Sulfolobus acidocaldarius DSM 639	Mutation(s): 0  Gene Names: cyp119, Saci_2081 EC: 1.14 (PDB Primary Data), 1.11.1.7 (PDB Primary Data)
UniProt
Find proteins for Q55080 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore Q55080  Go to UniProtKB:  Q55080

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	D [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
3SQ	C [auth A], F [auth B]	4-(4-fluorophenyl)-1H-imidazole C9 H7 F N2 QYDAFWKRBZYBOB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.801	α = 90
b = 95.458	β = 90
c = 106.715	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-02-18 
Deposition Author(s): Madrona, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2015-02-18
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Advisory, Author supporting evidence, Derived calculations, Other, Source and taxonomy
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Refinement description