8SBI | pdb_00008sbi

Crystal structure of human sterol 14 alpha-demethylase (CYP51) in the ligand-free state

PDB DOI: https://doi.org/10.2210/pdb8SBI/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes OPM

Deposited: 2023-04-03 Released: 2023-04-12
Deposition Author(s): Hargrove, T.Y., Wawrzak, Z., Lepesheva, G.I.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free:
0.246 (Depositor), 0.260 (DCC)
R-Value Work:
0.230 (Depositor), 0.230 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Unique Structural Features Relate to Evolutionary Adaptation of Cytochrome P450 in the Abyssal Zone

Hargrove, T.Y., Lamb, D.C., Wawrzak, Z., Minasov, G., Goldstone, J.V., Kelly, S.L., Stegeman, J.J., Lepesheva, G.I.

(2025) Int J Mol Sci 26

DOI: https://doi.org/10.3390/ijms26125689

Macromolecule Content

Total Structure Weight: 104.59 kDa
Atom Count: 7,299
Modeled Residue Count: 890
Deposited Residue Count: 906
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	453	Homo sapiens	Mutation(s): 2 Gene Names: CYP51A1, CYP51 EC: 1.14.14.154 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free: 0.246 (Depositor), 0.260 (DCC)
R-Value Work: 0.230 (Depositor), 0.230 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.81	α = 90
b = 55.64	β = 90
c = 103.07	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-04-12

Deposition Author(s):

Lepesheva, G.I.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM067871

Revision History (Full details and data files)

Version 1.0: 2023-04-12
Type: Initial release
Version 1.1: 2024-05-22
Changes: Data collection
Version 1.2: 2025-06-25
Changes: Database references, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.