3T3Z

Human Cytochrome P450 2E1 in complex with pilocarpine

• PDB DOI: https://doi.org/10.2210/pdb3T3Z/pdb

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


• Deposited: 2011-07-25 Released: 2011-12-07 
• Deposition Author(s): Meneely, K.M., DeVore, N.M., Scott, E.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.281 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 224.9 kDa 
• Atom Count: 16,204 
• Modelled Residue Count: 1,856 
• Deposited Residue Count: 1,904 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 2E1	A, B, C, D	476	Homo sapiens	Mutation(s): 0  Gene Names: CYP2E, CYP2E1 EC: 1.14.13
UniProt & NIH Common Fund Data Resources
Find proteins for P05181 (Homo sapiens) Explore P05181  Go to UniProtKB:  P05181
PHAROS:  P05181 GTEx:  ENSG00000130649

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	E, F, G, H	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	I [auth A], K [auth B], M [auth C], O [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
9PL	J [auth A], L [auth B], N [auth C], P [auth D]	(3S,4R)-3-ethyl-4-[(1-methyl-1H-imidazol-5-yl)methyl]dihydrofuran-2(3H)-one C11 H16 N2 O2 QCHFTSOMWOSFHM-WPRPVWTQSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9PL	Binding MOAD:  3T3Z	Ki: 7.65e+5 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	E, F, G, H	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.281 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.638	α = 90
b = 100.638	β = 90
c = 259.453	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): Meneely, K.M., DeVore, N.M., Scott, E.E.

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2012-06-06
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-29
  Changes: Data collection, Database references, Structure summary