Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 110.14 kDa 
• Atom Count: 7522 
• Modelled Residue Count: 889 
• Deposited Residue Count: 922 
• Unique protein chains: 1

3LD6

Crystal structure of human lanosterol 14alpha-demethylase (CYP51) in complex with ketoconazole

• PDB DOI: 10.2210/pdb3LD6/pdb
• Entry: 3LD6 supersedes: 3I3K

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


• Deposited: 2010-01-12 Released: 2010-02-02 
• Deposition Author(s): Strushkevich, N., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.275 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 

Literature

Structural basis of human CYP51 inhibition by antifungal azoles.

Strushkevich, N., Usanov, S.A., Park, H.W.

(2010) J Mol Biol 397: 1067-1078

• PubMed: 20149798 
• DOI: 10.1016/j.jmb.2010.01.075
• Primary Citation of Related Structures:  
  3JUS, 3JUV, 3LD6


• PubMed Abstract: 
  

The obligatory step in sterol biosynthesis in eukaryotes is demethylation of sterol precursors at the C14-position, which is catalyzed by CYP51 (sterol 14-alpha demethylase) in three sequential reactions. In mammals, the final product of the pathway is cholesterol, while important intermediates, meiosis-activating sterols, are produced by CYP51. Three crystal structures of human CYP51, ligand-free and complexed with antifungal drugs ketoconazole and econazole, were determined, allowing analysis of the molecular basis for functional conservation within the CYP51 family. Azole binding occurs mostly through hydrophobic interactions with conservative residues of the active site. The substantial conformational changes in the B' helix and F-G loop regions are induced upon ligand binding, consistent with the membrane nature of the protein and its substrate. The access channel is typical for mammalian sterol-metabolizing P450 enzymes, but is different from that observed in Mycobacterium tuberculosis CYP51. Comparison of the azole-bound structures provides insight into the relative binding affinities of human and bacterial P450 enzymes to ketoconazole and fluconazole, which can be useful for the rational design of antifungal compounds and specific modulators of human CYP51.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario, Canada. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lanosterol 14-alpha demethylase	A, B	461	Homo sapiens	Mutation(s): 0  Gene Names: CYP51, CYP51A1 EC: 1.14.13.70 (PDB Primary Data), 1.14.14.154 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q16850 (Homo sapiens) Explore Q16850  Go to UniProtKB:  Q16850
PHAROS:  Q16850 GTEx:  ENSG00000001630

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
Cycloheptakis-(1-4)-(alpha-D-glucopyranose)	C, D	7		N/A
Glycosylation Resources
GlyTouCan:  G01435GL GlyCosmos:  G01435GL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
KKK	F [auth A], H [auth B]	1-acetyl-4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine C26 H28 Cl2 N4 O4 XMAYWYJOQHXEEK-OZXSUGGESA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900012	C, D	beta-cyclodextrin	Oligosaccharide / Drug delivery		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.275 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.726	α = 90
b = 145.726	β = 90
c = 110.341	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-12 
• Released Date: 2010-02-02 
Deposition Author(s): Strushkevich, N., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Park, H., Structural Genomics Consortium (SGC)
• This entry supersedes: 3I3K

Revision History  

• Version 1.0: 2010-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2018-04-18
  Changes: Data collection
• 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