7XBN

Crystal Structure of YC-17-bound cytochrome P450 PikC with the unnatural amino acid p-Acetyl-L-Phenylalanine incorporated at position 238


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

New mechanistic insight of cytochrome P450 PikC gained from site-specific mutagenesis by non-coding amino acids

Pan, Y.J.Li, G.B.Gao, X.Li, S.Y.

(2023) Nat Commun 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 monooxygenase PikC
A, B
444Streptomyces venezuelaeMutation(s): 0 
Gene Names: pikCpicK
EC: 1.14.15.33
UniProt
Find proteins for O87605 (Streptomyces venezuelae)
Explore O87605 
Go to UniProtKB:  O87605
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO87605
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PXI (Subject of Investigation/LOI)
Query on PXI

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
4-{[4-(DIMETHYLAMINO)-3-HYDROXY-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL]OXY}-12-ETHYL-3,5,7,11-TETRAMETHYLOXACYCLODODEC-9-ENE-2,8-DIONE
C25 H43 N O6
DZGHWPQKGWXOHD-OYZFACIPSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
L [auth B],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
4AF
Query on 4AF
A, B
L-PEPTIDE LINKINGC11 H13 N O3PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.823α = 90
b = 108.903β = 90
c = 152.63γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32000039
National Natural Science Foundation of China (NSFC)China32025001
National Natural Science Foundation of China (NSFC)China31872729

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2023-11-29
    Changes: Refinement description