3LD6

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

PDB DOI: https://doi.org/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)

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 110.14 kDa
Atom Count: 7,522
Modelled Residue Count: 889
Deposited Residue Count: 922
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16850
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
Cycloheptakis-(1-4)-(alpha-D-glucopyranose)	C, D	7		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G01435GL GlyCosmos: G01435GL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B]	E [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
KKK Query on KKK Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B]	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		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900012 Query on PRD_900012	C, D	beta-cyclodextrin	Oligosaccharide / Drug delivery		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-02-02

Deposition Author(s):

Structural Genomics Consortium (SGC)

This entry supersedes: 3I3K

Revision History (Full details and data files)

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
Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

3LD6

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2