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- PDB-1v1d: Nucleophilic and General Acid Catalysis at Physiological pH by a ... -

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Basic information

Entry
Database: PDB / ID: 1v1d
TitleNucleophilic and General Acid Catalysis at Physiological pH by a Designed Miniature Esterase
ComponentsPANCREATIC HORMONE
KeywordsHORMONE / CLEAVAGE ON PAIR OF BASIC RESIDUES / PANCREAS
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
Pancreatic polypeptide prohormone
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodSOLUTION NMR / simulated annealing
AuthorsNicoll, A. / Allemann, R.K.
CitationJournal: Org.Biomol.Chem. / Year: 2004
Title: Nucleophilic and General Acid Catalysis at Physiological Ph by a Designed Miniature Esterase
Authors: Nicoll, A. / Allemann, R.K.
History
DepositionApr 14, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PANCREATIC HORMONE


Theoretical massNumber of molelcules
Total (without water)3,6881
Polymers3,6881
Non-polymers00
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 / 20NO VIOLATIONS
Representative

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Components

#1: Protein/peptide PANCREATIC HORMONE / PANCREATIC POLYPEPTIDE / PP


Mass: 3688.110 Da / Num. of mol.: 1 / Fragment: PANCREATIC POLYPEPTIDE RESIDUES 30-60 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) BOS TAURUS (cattle) / References: UniProt: P01302
Compound detailsCHAIN A ENGINEERED MUTATION ALA47HIS, ALA51HIS,GLU52GLN
Sequence detailsMUTATIONS: A18H, A22H, E23Q

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY/TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING STANDARD EXPERIMENTAL TECHNIQUES

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Sample preparation

Sample conditionsIonic strength: 100 mM / pH: 5.0 / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
CNSstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: NO VIOLATIONS / Conformers calculated total number: 20 / Conformers submitted total number: 20

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