9MDV | pdb_00009mdv

Apo form of the estrogen receptor alpha ligand binding domain of Melanotaenia fluviatilis

• PDB DOI: https://doi.org/10.2210/pdb9MDV/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Melanotaenia fluviatilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-12-05 Released: 2025-10-22 
• Deposition Author(s): Pederick, J.L., McDougal, D.P., Bruning, J.B.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.286 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

Apo form of the estrogen receptor alpha ligand binding domain of Melanotaenia fluviatilis

Pederick, J.L., McDougal, D.P., Bruning, J.B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 57.8 kDa 
• Atom Count: 4,097 
• Modeled Residue Count: 477 
• Deposited Residue Count: 502 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	251	Melanotaenia fluviatilis	Mutation(s): 0  Gene Names: ESR1
UniProt
Find proteins for D6N7U3 (Melanotaenia fluviatilis) Explore D6N7U3  Go to UniProtKB:  D6N7U3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B], E [auth B], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.286 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.374	α = 90
b = 94.507	β = 96.86
c = 60.954	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Pederick, J.L., McDougal, D.P., Bruning, J.B.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP230100609

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release