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- PDB-2na5: NMR solution structure of vitamin B12 conjugates of PYY3-36 -

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Basic information

Entry
Database: PDB / ID: 2na5
TitleNMR solution structure of vitamin B12 conjugates of PYY3-36
ComponentsPeptide YY
KeywordsHORMONE / vitamin-peptide conjugate
Function / homology
Function and homology information


neuropeptide Y receptor binding / intestinal epithelial cell differentiation / neuropeptide hormone activity / feeding behavior / neuropeptide signaling pathway / Peptide ligand-binding receptors / G protein-coupled receptor binding / hormone activity / G alpha (i) signalling events / extracellular space / extracellular region
Similarity search - Function
Pancreatic hormone-like / Pancreatic hormone-like, conserved site / Pancreatic hormone peptide / Pancreatic hormone family signature. / Pancreatic hormone family profile. / Pancreatic hormones / neuropeptide F / peptide YY family
Similarity search - Domain/homology
CYANOCOBALAMIN / Peptide YY
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsDoyle, R.P. / Henry, K.E. / Roth, C.L. / Kerwood, D.J. / Allis, D.G. / Holz, G.G. / Zubieta, J.
CitationJournal: Chemmedchem / Year: 2016
Title: Solution Structure and Constrained Molecular Dynamics Study of Vitamin B12 Conjugates of the Anorectic Peptide PYY(3-36).
Authors: Henry, K.E. / Kerwood, D.J. / Allis, D.G. / Workinger, J.L. / Bonaccorso, R.L. / Holz, G.G. / Roth, C.L. / Zubieta, J. / Doyle, R.P.
History
DepositionDec 21, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Other
Revision 2.0Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nmr_software / pdbx_validate_chiral / struct_conn / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nmr_software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide YY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5072
Polymers4,1511
Non-polymers1,3561
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 4structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Peptide YY / PYY / PYY-I / Peptide tyrosine tyrosine / Peptide YY(3-36) / PYY-II


Mass: 4150.594 Da / Num. of mol.: 1 / Fragment: residues 31-64 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10082
#2: Chemical ChemComp-CNC / CYANOCOBALAMIN


Mass: 1356.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C63H89CoN14O14P
Nonpolymer detailsTHE DEPOSITORS STATE THAT WHILE ACTUALLY COVALENTLY LINKED BETWEEN THE VITAMIN B12 AND PYY3-36, ...THE DEPOSITORS STATE THAT WHILE ACTUALLY COVALENTLY LINKED BETWEEN THE VITAMIN B12 AND PYY3-36, THIS ENTRY DISPLAYS THE SYSTEM SEPARATED BETWEEN NZ2 AND C5R TO PRODUCE A SMALLER MODIFIED LYS AND AN ACIDIC VITAMIN B12 IN ACCORDANCE WITH PDB ANNOTATION POLICIES.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY

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Sample preparation

DetailsContents: 1 mM vitamin B12 conjugate of PYY3, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: vitamin B12 conjugate of PYY3-36-1
Sample conditionspH: 5.5 / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinchemical shift calculation
TopSpin1.3Bruker Biospinchemical shift assignment
GROMOS96Schwede et al.refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: 2D NOE cross peaks were categorized as strong, medium, or weak and distance constraints were set to 1.8 to 3.5A, 1.8 to 4.5A and 1.8 to 6.0A.
NMR constraintsNOE constraints total: 179 / NOE intraresidue total count: 104 / NOE long range total count: 5 / NOE medium range total count: 23 / NOE sequential total count: 46
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 4 / Conformers submitted total number: 1

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