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- PDB-1atd: HIGH-RESOLUTION STRUCTURE OF ASCARIS TRYPSIN INHIBITOR IN SOLUTIO... -

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Basic information

Entry
Database: PDB / ID: 1atd
TitleHIGH-RESOLUTION STRUCTURE OF ASCARIS TRYPSIN INHIBITOR IN SOLUTION: DIRECT EVIDENCE FOR A PH INDUCED CONFORMATIONAL TRANSITION IN THE REACTIVE SITE
ComponentsASCARIS TRYPSIN INHIBITOR
KeywordsPROTEINASE INHIBITOR(TRYPSIN)
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / Laminin / Laminin / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesAscaris suum (pig roundworm)
MethodSOLUTION NMR
AuthorsClore, G.M. / Grasberger, B.L. / Gronenborn, A.M.
Citation
Journal: Structure / Year: 1994
Title: High-resolution structure of Ascaris trypsin inhibitor in solution: direct evidence for a pH-induced conformational transition in the reactive site.
Authors: Grasberger, B.L. / Clore, G.M. / Gronenborn, A.M.
#1: Journal: Biochemistry / Year: 1990
Title: Sequential Resonance Assignment and Secondary Structure Determination of the Ascaris Trypsin Inhibitor, a Member of a Novel Class of Proteinase Inhibitors
Authors: Gronenborn, A.M. / Nilges, M. / Peanasky, R.J. / Clore, G.M.
History
DepositionMay 20, 1994Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 9, 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: ASCARIS TRYPSIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)6,8081
Polymers6,8081
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)32 / -
Representative

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Components

#1: Protein ASCARIS TRYPSIN INHIBITOR


Mass: 6807.853 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ascaris suum (pig roundworm) / References: UniProt: P19398
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

RefinementSoftware ordinal: 1
Details: THE 3D STRUCTURE OF THE PH 4.75 FORM OF THE ASCARIS TRYPSIN INHIBITOR IN SOLUTION BY NMR IS BASED ON 1078 EXPERIMENTAL RESTRAINTS COMPRISING: 43 SHORT RANGE (1 < |I-J| 5) INTERRESIDUE ...Details: THE 3D STRUCTURE OF THE PH 4.75 FORM OF THE ASCARIS TRYPSIN INHIBITOR IN SOLUTION BY NMR IS BASED ON 1078 EXPERIMENTAL RESTRAINTS COMPRISING: 43 SHORT RANGE (1 < |I-J| <=5) AND 218 LONG RANGE (|I-J|>5) INTERRESIDUE INTERPROTON DISTANCE RESTRAINTS, 320 INTRARESIDUE INTERPROTON DISTANCE RESTRAINTS, 48 DISTANCE RESTRAINTS FOR 4 HYDROGEN BONDS, AND 59 PHI, 49 PSI AND 41 CHI1 TORSION ANGLE RESTRAINTS. A COMPLETE LIST OF EXPERIMENTAL RESTRAINTS HAS BEEN DEPOSITED WITH THE BROOKHAVEN DATA BANK. THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. & GRONENBORN, A.M. (1988) FEBS LETT 29, 317-324 ALL STRUCTURAL STATISTICS ARE GIVEN IN REFERENCE 1. THE RESTRAINED MINIMIZED AVERAGE STRUCTURE (SA)R IS PRESENTED IN PROTEIN DATA BANK ENTRY 1ATA. THIS IS OBTAINED BY FIRST AVERAGING THE COORDINATES OF THE INDIVIDUAL 32 DYNAMICAL SIMULATED ANNEALING SA STRUCTURES BEST FITTED TO RESIDUES 5 - 60, AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. THE QUANTITY PRESENTED IN COLUMNS 61 - 66 IN ENTRY 1ATA (THE B VALUE FIELD IN X-RAY STRUCTURES) GIVES THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SA STRUCTURES AND THE MEAN STRUCTURE. THE QUANTITIES IN THIS FIELD OF THE INDIVIDUAL STRUCTURES IN THIS ENTRY HAVE NO MEANING.
NMR ensembleConformers submitted total number: 32

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