7A3Y | pdb_00007a3y

RNA duplex with a cytosine bulge in complex with berberine

PDB DOI: https://doi.org/10.2210/pdb7A3Y/pdb
BMRB: 34553
NAKB: 7A3Y

Classification: RNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2020-08-19 Released: 2021-03-10
Deposition Author(s): Podbevsek, P., Plavec, J.
Funding Organization(s): Slovenian Research Agency

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 10
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

Validation slider image for 7A3Y

This is version 1.2 of the entry. See complete history.

Literature

Interaction between berberine and RNA for the exploration of phytochemicals role

Podbevsek, P., Plavec, J.

(2021) Nucleic Acids Res

Macromolecule Content

Total Structure Weight: 8.3 kDa
Atom Count: 551
Modeled Residue Count: 25
Deposited Residue Count: 25
Unique nucleic acid chains: 2

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
RNA-A chain A	A	13	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 2
RNA-A chain B	B	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BER (Subject of Investigation/LOI) Query on BER Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	BERBERINE C₂₀ H₁₈ N O₄ YBHILYKTIRIUTE-UHFFFAOYSA-N		Interactions Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 10
Selection Criteria: structures with the lowest energy

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-03-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Slovenian Research Agency	Slovenia	P1-0242

Revision History (Full details and data files)

Version 1.0: 2021-03-10
Type: Initial release
Version 1.1: 2023-06-14
Changes: Database references, Other
Version 1.2: 2024-06-19
Changes: Data collection, Database references

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.