7OTD | pdb_00007otd

Oxytocin NMR solution structure

• PDB DOI: https://doi.org/10.2210/pdb7OTD/pdb
• BMRB: 34637

• Classification: HORMONE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2021-06-10 Released: 2021-10-13 
• Deposition Author(s): Shalev, D.E., Alshanski, I., Yitzchaik, S., Hurevich, M.
• Funding Organization(s): European Union (EU)

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Experimental Data Snapshot

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

Literature

Determining the structure and binding mechanism of oxytocin-Cu 2+ complex using paramagnetic relaxation enhancement NMR analysis.

Alshanski, I., Shalev, D.E., Yitzchaik, S., Hurevich, M.

(2021) J Biol Inorg Chem 26: 809-815

• PubMed: 34459989 
• DOI: https://doi.org/10.1007/s00775-021-01897-1
• Primary Citation Related Structures: 
  7OFG, 7OTD


• PubMed Abstract: 
  

  Oxytocin is a neuropeptide that binds copper ions in nature. The structure of oxytocin in interaction with Cu ²⁺ was determined here by NMR, showing which atoms of the peptide are involved in binding. Paramagnetic relaxation enhancement NMR analyses indicated a binding mechanism where the amino terminus was required for binding and subsequently Tyr2, Ile3 and Gln4 bound in that order. The aromatic ring of Tyr2 formed a π-cation interaction with Cu ²⁺ . Oxytocin copper complex structure revealed by paramagnetic relaxation enhancement NMR analyses.

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Organizational Affiliation: 
• Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel.
Department of Pharmaceutical Engineering, Azrieli College of Engineering Jerusalem, 91035, Jerusalem, Israel. [e-mail].
Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel. [e-mail].
Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel. [e-mail].
Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904, Jerusalem, Israel. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: NMR relaxation study

Macromolecule Content 

• Total Structure Weight: 1.09 kDa 
• Atom Count: 70 
• Modeled Residue Count: 9 
• Deposited Residue Count: 9 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UNK-TYR-ILE-GLN-ASN-CYS-PRO-LEU-GLY	A	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01178 (Homo sapiens) Explore P01178  Go to UniProtKB:  P01178
PHAROS:  P01178 GTEx:  ENSG00000101405

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
NH2	C [auth A]	AMINO GROUP H2 N QGZKDVFQNNGYKY-UHFFFAOYSA-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: 2021-10-13 
Deposition Author(s): Shalev, D.E., Alshanski, I., Yitzchaik, S., Hurevich, M.

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Funding Organization	Location	Grant Number
European Union (EU)	Israel	664786

Revision History  

• Version 1.0: 2021-10-13
  Type: Initial release