3DL9 | pdb_00003dl9

Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2

PDB DOI: https://doi.org/10.2210/pdb3DL9/pdb

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

Deposited: 2008-06-26 Released: 2008-08-05
Deposition Author(s): Strushkevich, N.V., Tempel, W., Gilep, A.A., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Wilkstrom, M., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free:
0.218 (Depositor), 0.219 (DCC)
R-Value Work:
0.183 (Depositor), 0.189 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2.

Strushkevich, N.V., Tempel, W., Gilep, A.A., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Wilkstrom, M., Bochkarev, A., Park, H.

To be published.

Macromolecule Content

Total Structure Weight: 114.65 kDa
Atom Count: 7,959
Modeled Residue Count: 932
Deposited Residue Count: 958
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 2R1	A, B	479	Homo sapiens	Mutation(s): 0 Gene Names: CYP2R1 EC: 1.14.14 (PDB Primary Data), 1.14.14.24 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6VVX0 (Homo sapiens) Explore Q6VVX0 Go to UniProtKB: Q6VVX0
PHAROS: Q6VVX0 GTEx: ENSG00000186104
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6VVX0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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] mmCIF format, chain E [auth A] mmCIF 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]
V2H Query on V2H 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] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B]	F [auth A], H [auth B]	(1S,3R,5Z,7E,22E)-9,10-secoergosta-5,7,10,22-tetraene-1,3-diol C₂₈ H₄₄ O₂ HKXBNHCUPKIYDM-CGMHZMFXSA-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: 2.72 Å
R-Value Free: 0.218 (Depositor), 0.219 (DCC)
R-Value Work: 0.183 (Depositor), 0.189 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.303	α = 90
b = 163.04	β = 90
c = 152.588	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-3000	data reduction
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-08-05

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-08-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
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: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary