Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 56.32 kDa 
• Atom Count: 3,741 
• Modelled Residue Count: 455 
• Deposited Residue Count: 485 
• Unique protein chains: 1

 1W0G

Crystal structure of human cytochrome P450 3A4

• PDB DOI:  https://doi.org/10.2210/pdb1W0G/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-06-03 Released: 2004-07-22 
• Deposition Author(s): Williams, P.A., Cosme, J., Vinkovic, D.M., Ward, A., Angove, H.C., Day, P.J., Vonrhein, C., Tickle, I.J., Jhoti, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 0.318 
• R-Value Work: 0.234 
• R-Value Observed: 0.238 

Literature

Crystal Structures of Human Cytochrome P450 3A4 Bound to Metyrapone and Progesterone

Williams, P.A., Cosme, J., Vinkovic, D.M., Ward, A., Angove, H.C., Day, P.J., Vonrhein, C., Tickle, I.J., Jhoti, H.

(2004) Science 305: 683

• PubMed: 15256616 
• DOI: https://doi.org/10.1126/science.1099736
• Primary Citation of Related Structures:  
  1W0E, 1W0F, 1W0G


• PubMed Abstract: 
  

Cytochromes P450 (P450s) metabolize a wide range of endogenous compounds and xenobiotics, such as pollutants, environmental compounds, and drug molecules. The microsomal, membrane-associated, P450 isoforms CYP3A4, CYP2D6, CYP2C9, CYP2C19, CYP2E1, and CYP1A2 are responsible for the oxidative metabolism of more than 90% of marketed drugs. Cytochrome P450 3A4 (CYP3A4) metabolizes more drug molecules than all other isoforms combined. Here we report three crystal structures of CYP3A4: unliganded, bound to the inhibitor metyrapone, and bound to the substrate progesterone. The structures revealed a surprisingly small active site, with little conformational change associated with the binding of either compound. An unexpected peripheral binding site is identified, located above a phenylalanine cluster, which may be involved in the initial recognition of substrates or allosteric effectors.

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Organizational Affiliation: 

Astex Technology, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME P450 3A4	A	485	Homo sapiens	Mutation(s): 0  Gene Names: CYP3A4, CYP3A3 EC: 1.14.13.67 (PDB Primary Data), 1.14.14.1 (PDB Primary Data), 1.14.14.56 (UniProt), 1.14.14.73 (UniProt), 1.14.14.55 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P08684 (Homo sapiens) Explore P08684  Go to UniProtKB:  P08684
PHAROS:  P08684

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
MYT	B [auth A]	METYRAPONE C14 H14 N2 O FJLBFSROUSIWMA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MYT	BindingDB:  1W0G	IC50: min: 3000, max: 4932 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 0.318 
• R-Value Work: 0.234 
• R-Value Observed: 0.238 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.94	α = 90
b = 100.91	β = 90
c = 131	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-22 
Deposition Author(s): Williams, P.A., Cosme, J., Vinkovic, D.M., Ward, A., Angove, H.C., Day, P.J., Vonrhein, C., Tickle, I.J., Jhoti, H.

Revision History  

• Version 1.0: 2004-07-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance