21CC | pdb_000021cc

A solution NMR model of L-RNA r(UAGGGUUAGGGU) bounding Protoporphyrin IX ligand

• PDB DOI: https://doi.org/10.2210/pdb21CC/pdb
• NAKB: 21CC

• Classification: RNA
• Organism(s): chemical production metagenome
• Mutation(s): No 


• Deposited: 2025-12-07 Released: 2025-12-17 
• Deposition Author(s): Iwakiri, R., Wang, S.Y., Xu, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

A solution NMR model of L-RNA r(UAGGGUUAGGGU) bounding Protoporphyrin IX ligand

Iwakiri, R., Wang, S.Y., Xu, Y.

To be published.

Biological Assembly 1  

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

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 8.38 kDa 
• Atom Count: 560 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3')	A, B	12	chemical production metagenome

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PP9	C [auth B]	PROTOPORPHYRIN IX C34 H34 N4 O4 FEDYMSUPMFCVOD-UJJXFSCMSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Iwakiri, R., Wang, S.Y., Xu, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release