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- PDB-1brb: CRYSTAL STRUCTURES OF RAT ANIONIC TRYPSIN COMPLEXED WITH THE PROT... -

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Basic information

Entry
Database: PDB / ID: 1brb
TitleCRYSTAL STRUCTURES OF RAT ANIONIC TRYPSIN COMPLEXED WITH THE PROTEIN INHIBITORS APPI AND BPTI
Components
  • PANCREATIC TRYPSIN INHIBITOR
  • TRYPSIN
KeywordsCOMPLEX(PROTEINASE/INHIBITOR) / COMPLEX(PROTEINASE-INHIBITOR) / COMPLEX(PROTEINASE-INHIBITOR) complex
Function / homology
Function and homology information


Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / Neutrophil degranulation ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / Neutrophil degranulation / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / collagen catabolic process / trypsin / serine protease inhibitor complex / digestion / response to nutrient / serine-type endopeptidase inhibitor activity / protease binding / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region
Similarity search - Function
: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily ...: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / : / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Anionic trypsin-2 / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsPerona, J.J. / Fletterick, R.J.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Crystal structures of rat anionic trypsin complexed with the protein inhibitors APPI and BPTI.
Authors: Perona, J.J. / Tsu, C.A. / Craik, C.S. / Fletterick, R.J.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Relocating a Negative Charge in the Binding Pocket of Trypsin
Authors: Perona, J.J. / Tsu, C.A. / Mcgrath, M.E. / Craik, C.S. / Fletterick, R.J.
History
DepositionDec 17, 1992Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: TRYPSIN
I: PANCREATIC TRYPSIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)30,2222
Polymers30,2222
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-8 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.650, 92.650, 62.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TRYPSIN


Mass: 23814.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / References: UniProt: P00763, trypsin
#2: Protein PANCREATIC TRYPSIN INHIBITOR


Mass: 6407.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P00974
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE BPTI INHIBITOR IS THE VARIANT C5A/C55A PRODUCED BY RECOMBINANT DNA METHODOLOGIES AND EXPRESSED ...THE BPTI INHIBITOR IS THE VARIANT C5A/C55A PRODUCED BY RECOMBINANT DNA METHODOLOGIES AND EXPRESSED IN ESCHERICHIA COLI (ALTMAN,J.; PH. D. THESIS, UNIVERSITY OF CALIFORNIA AT SAN FRANCISCO, 1991). THE N-TERMINAL FOUR RESIDUES AND THE C-TERMINAL THREE RESIDUES (56 - 58) ARE DISORDERED.
Has protein modificationY
Sequence detailsSEQUENCE ADVISORY NOTICE: SEQUENCE FOR TRYPSIN IN THIS STRUCTURE WAS TAKEN FROM GENEMBL WHICH ...SEQUENCE ADVISORY NOTICE: SEQUENCE FOR TRYPSIN IN THIS STRUCTURE WAS TAKEN FROM GENEMBL WHICH DIFFERS FROM SWISSPROT SEQUENCE AT POSITIONS 61 AND 65. SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: TRY2_RAT SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ASP 84 ASN E 79 (SWISSPROT ERROR) ILE 88 VAL E 83 (SWISSPROT ERROR) ASP 194 GLY E 189 (ENGINEERED) GLY 227 ASP E 226 (ENGINEERED) SWISS-PROT ENTRY NAME: BPT1_BOVIN SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE CYS 40 ALA I 5 (VARIANT) LEU 41 GLY I 6 CYS 90 ALA I 55 (VARIANT)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme1drop
230-45 %PEG33501reservoir
30.2 Mammonium acetate1reservoir
40.1 Msodium citrate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 17414 / % possible obs: 93 % / Num. measured all: 66494 / Rmerge(I) obs: 0.097

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.198 / Rfactor obs: 0.198 / Highest resolution: 2.1 Å
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 0 142 2184
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.8

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