4JYG

Crystal structure of RARbeta LBD in complex with agonist BMS411 [4-{[(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)carbonyl]amino}benzoic acid]

Structural Biology Knowledgebase: 4JYG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JYG

Classification: Transcription / Agonist

Total Structure Weight: 64916.69

Macromolecule Entities
Molecule Chains Length Organism Details
Retinoic acid receptor beta A, B 267 Homo sapiens Fragment: Ligand binding domain, UNP residues 176-421
Mutation: L407M
Gene Name(s): RARB Gene View HAP NR1B2
Steroid Receptor Coactivator 1 F, G 13 Homo sapiens EC#: 2.3.1.48 IUBMB
Fragment: UNP residues 686-698
Gene Name(s): NCOA1 Gene View BHLHE74 SRC1

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1NY
Query on 1NY

A, B 4-{[(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen- 2-yl)carbonyl]amino}benzoic acid
C26 H23 N O3
AZQWAFBHDUNJHM-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PE4
Query on PE4

B 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]- ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
POLYETHYLENE GLYCOL PEG4000 (Synonym)
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FLC
Query on FLC

G CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.199
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 58.24 α = 90.00
b = 84.83 β = 90.00
c = 108.42 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-03-29
  • Released Date: 2014-03-19
  • Deposition author(s): Nadendla, E.K., Teyssier, C., Germain, P., Delfosse, V., Bourguet, W.

Revision History

  • 2016-04-13
    Type: Citation | Details: Citation update