9ECF | pdb_00009ecf

Crystal structure of the hERbeta LBD complexed with androstenediol and SRC 2-2 peptide (crystal form 2)

PDB DOI: https://doi.org/10.2210/pdb9ECF/pdb

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

Deposited: 2024-11-14 Released: 2025-11-19
Deposition Author(s): Pederick, J.L., Bruning, J.B.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.278 (Depositor), 0.278 (DCC)
R-Value Work:
0.250 (Depositor), 0.251 (DCC)
R-Value Observed:
0.252 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the hERbeta LBD complexed with androstenediol and SRC 2-2 peptide

Pederick, J.L., Bruning, J.B.

To be published.

Macromolecule Content

Total Structure Weight: 239.52 kDa
Atom Count: 14,712
Modeled Residue Count: 1,813
Deposited Residue Count: 2,080
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor beta	A [auth E] B [auth F] E [auth A] F [auth B] I A [auth E], B [auth F], E [auth A], F [auth B], I, J, M, N	247	Homo sapiens	Mutation(s): 0 Gene Names: ESR2, ESTRB, NR3A2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92731 (Homo sapiens) Explore Q92731 Go to UniProtKB: Q92731
PHAROS: Q92731 GTEx: ENSG00000140009
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92731
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2	C [auth G] D [auth H] G [auth C] H [auth D] K C [auth G], D [auth H], G [auth C], H [auth D], K, L, O, P	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596 Go to UniProtKB: Q15596
PHAROS: Q15596 GTEx: ENSG00000140396
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15596
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B81 (Subject of Investigation/LOI) Query on B81 Download Ideal Coordinates CCD File SDF format, chain Q [auth E] SDF format, chain R [auth F] SDF format, chain U [auth I] SDF format, chain X [auth N] SDF format, chain W [auth M] SDF format, chain V [auth J] SDF format, chain T [auth B] SDF format, chain S [auth A] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] MOL2 format, chain U [auth I] MOL2 format, chain X [auth N] MOL2 format, chain W [auth M] MOL2 format, chain V [auth J] MOL2 format, chain T [auth B] MOL2 format, chain S [auth A] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F] mmCIF format, chain U [auth I] mmCIF format, chain X [auth N] mmCIF format, chain W [auth M] mmCIF format, chain V [auth J] mmCIF format, chain T [auth B] mmCIF format, chain S [auth A]	Q [auth E] R [auth F] S [auth A] T [auth B] U [auth I] Q [auth E], R [auth F], S [auth A], T [auth B], U [auth I], V [auth J], W [auth M], X [auth N]	(3alpha,8alpha,17beta)-androst-5-ene-3,17-diol C₁₉ H₃₀ O₂ QADHLRWLCPCEKT-LOVVWNRFSA-N		Interactions Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth A] Focus chain T [auth B] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth M] Focus chain X [auth N] Interactions & Density Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth A] Focus chain T [auth B] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth M] Focus chain X [auth N]