2ABI | pdb_00002abi

Crystal structure of the human mineralocorticoid receptor ligand-binding domain bound to deoxycorticosterone

PDB DOI: https://doi.org/10.2210/pdb2ABI/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-07-15 Released: 2006-07-25
Deposition Author(s): Huyet, J., Pinon, G.-M., Rochel, M., Mayer, C., Rafestin-Oblin, M.-E., Fagart, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.264 (Depositor), 0.250 (DCC)
R-Value Work:
0.207 (Depositor), 0.200 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the human mineralocorticoid receptor ligand-binding domain bound to deoxycorticosterone

Huyet, J., Pinon, G.-M., Rochel, M., Mayer, C., Rafestin-Oblin, M.-E., Fagart, J.

To be published.

Macromolecule Content

Total Structure Weight: 90.02 kDa
Atom Count: 6,075
Modeled Residue Count: 698
Deposited Residue Count: 768
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mineralocorticoid receptor	A, B, C	256	Homo sapiens	Mutation(s): 1 Gene Names: NR3C2, MCR, MLR
UniProt & NIH Common Fund Data Resources
Find proteins for P08235 (Homo sapiens) Explore P08235 Go to UniProtKB: P08235
PHAROS: P08235 GTEx: ENSG00000151623
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08235
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1CA Query on 1CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	DESOXYCORTICOSTERONE C₂₁ H₃₀ O₃ ZESRJSPZRDMNHY-YFWFAHHUSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.264 (Depositor), 0.250 (DCC)
R-Value Work: 0.207 (Depositor), 0.200 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.77	α = 90
b = 119.77	β = 90
c = 41.5	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
BEAST	model building
CNS	refinement
BEAST	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-07-25

Deposition Author(s):

Rafestin-Oblin, M.-E.

Revision History (Full details and data files)

Version 1.0: 2006-07-25
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-10-25
Changes: Data collection, Refinement description

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.