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- PDB-2h3t: trans-(4-aminomethyl)phenylazobenzoic acid-aPP bound to DPC micelles -

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Basic information

Entry
Database: PDB / ID: 2h3t
Titletrans-(4-aminomethyl)phenylazobenzoic acid-aPP bound to DPC micelles
Components(Pancreatic hormone) x 2
KeywordsDE NOVO PROTEIN / photoswitch / pp folding
Function / homology
Function and homology information


neuropeptide Y receptor binding / neuropeptide hormone activity / feeding behavior / neuropeptide signaling pathway / extracellular space
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
Chem-EAB / Pancreatic polypeptide
Similarity search - Component
MethodSOLUTION NMR / torsion angle dynamics
AuthorsJurt, S. / Aemissegger, A. / Guentert, P. / Zerbe, O. / Hilvert, D.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2006
Title: A Photoswitchable Miniprotein Based on the Sequence of Avian Pancreatic Polypeptide
Authors: Jurt, S. / Aemissegger, A. / Guentert, P. / Zerbe, O. / Hilvert, D.
History
DepositionMay 23, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pancreatic hormone
B: Pancreatic hormone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2273
Polymers3,9572
Non-polymers2691
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Pancreatic hormone / Pancreatic polypeptide / aPP


Mass: 902.948 Da / Num. of mol.: 1 / Fragment: Pancreatic hormone, residues 1-9 / Source method: obtained synthetically
Details: synthesized by solid-phase peptide synthesis, derivativce of avian PP; residues 10-12 of avian pancreatic polyppetide (aPP) are replaced by trans-(4-aminomethyl)phenylazobenzoic acid-aPP.
References: UniProt: P68249
#2: Protein/peptide Pancreatic hormone / Pancreatic polypeptide / aPP


Mass: 3054.441 Da / Num. of mol.: 1 / Fragment: Pancreatic hormone, residues 11-34 / Source method: obtained synthetically
Details: synthesized by solid-phase peptide synthesis, derivativce of avian PP; residues 10-12 of avian pancreatic polyppetide (aPP) are replaced by trans-(4-aminomethyl)phenylazobenzoic acid-aPP.
References: UniProt: P68249
#3: Chemical ChemComp-EAB / (3-{(E)-[3-(AMINOMETHYL)PHENYL]DIAZENYL}PHENYL)ACETIC ACID


Mass: 269.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15N3O2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1212D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2mM peptide; 300mM DPC; 50mM MES buffer(pH 6.0); 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 6 / Pressure: AMBIENT / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.2.2Guentert, P. et al.refinement
CYANA2.2.2Guentert, P. et al.structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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