2BAW | pdb_00002baw

Human Nuclear Receptor-Ligand Complex 1

PDB DOI: https://doi.org/10.2210/pdb2BAW/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-10-15 Released: 2006-01-24
Deposition Author(s): Fyffe, S.A., Alphey, M.S., Buetow, L., Smith, T.K., Ferguson, M.A.J., Sorensen, M.D., Bjorkling, F., Hunter, W.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.276 (Depositor), 0.280 (DCC)
R-Value Work:
0.245 (Depositor), 0.240 (DCC)
R-Value Observed:
0.245 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2GWX

Literature

Reevaluation of the PPAR-beta/delta Ligand Binding Domain Model Reveals Why It Exhibits the Activated Form

Fyffe, S.A., Alphey, M.S., Buetow, L., Smith, T.K., Ferguson, M.A.J., Sorensen, M.D., Bjorkling, F., Hunter, W.N.

(2006) Mol Cell 21: 1-2

PubMed: 16387648 Search on PubMed
DOI: https://doi.org/10.1016/j.molcel.2005.12.001
Primary Citation of Related Structures:
2BAW

Organizational Affiliation

Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.

Macromolecule Content

Total Structure Weight: 62.26 kDa
Atom Count: 4,224
Modeled Residue Count: 498
Deposited Residue Count: 534
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator activated receptor delta	A, B	267	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q03181 (Homo sapiens) Explore Q03181 Go to UniProtKB: Q03181
PHAROS: Q03181 GTEx: ENSG00000112033
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03181
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VCA Query on VCA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	VACCENIC ACID C₁₈ H₃₄ O₂ UWHZIFQPPBDJPM-FPLPWBNLSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]
B7G Query on B7G Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	heptyl beta-D-glucopyranoside C₁₃ H₂₆ O₆ NIDYWHLDTIVRJT-UJPOAAIJSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.276 (Depositor), 0.280 (DCC)
R-Value Work: 0.245 (Depositor), 0.240 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.77	α = 90
b = 94.22	β = 97.77
c = 96.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-01-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-01-24
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2011-09-28
Changes: Database references
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.5: 2024-03-13
Changes: Data collection, Database references, Structure summary