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- PDB-2kai: REFINED 2.5 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF THE COMPLEX FORM... -

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Basic information

Entry
Database: PDB / ID: 2kai
TitleREFINED 2.5 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF THE COMPLEX FORMED BY PORCINE KALLIKREIN A AND THE BOVINE PANCREATIC TRYPSIN INHIBITOR. CRYSTALLIZATION, PATTERSON SEARCH, STRUCTURE DETERMINATION, REFINEMENT, STRUCTURE AND COMPARISON WITH ITS COMPONENTS AND WITH THE BOVINE TRYPSIN-PANCREATIC TRYPSIN INHIBITOR COMPLEX
Components
  • (KALLIKREIN A) x 2
  • BOVINE PANCREATIC TRYPSIN INHIBITOR
KeywordsCOMPLEX (PROTEINASE-INHIBITOR)
Function / homology
Function and homology information


tissue kallikrein / trypsinogen activation / negative regulation of serine-type endopeptidase activity / regulation of systemic arterial blood pressure / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / zymogen activation / molecular function inhibitor activity ...tissue kallikrein / trypsinogen activation / negative regulation of serine-type endopeptidase activity / regulation of systemic arterial blood pressure / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / zymogen activation / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / secretory granule / serine-type endopeptidase inhibitor activity / protease binding / serine-type endopeptidase activity / calcium ion binding / extracellular space
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 / Few Secondary Structures ...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 domain profile. / Serine proteases, trypsin family, serine active site. / 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
Glandular kallikrein / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesSus scrofa (pig)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBode, W. / Chen, Z.
Citation
Journal: J.Mol.Biol. / Year: 1983
Title: Refined 2.5 A X-ray crystal structure of the complex formed by porcine kallikrein A and the bovine pancreatic trypsin inhibitor. Crystallization, Patterson search, structure determination, ...Title: Refined 2.5 A X-ray crystal structure of the complex formed by porcine kallikrein A and the bovine pancreatic trypsin inhibitor. Crystallization, Patterson search, structure determination, refinement, structure and comparison with its components and with the bovine trypsin-pancreatic trypsin inhibitor complex
Authors: Chen, Z. / Bode, W.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: Refined 2 Angstroms X-Ray Crystal Structure of Porcine Pancreatic Kallikrein A, a Specific Trypsin-Like Serine Proteinase. Crystallization, Structure Determination,Crystallographic ...Title: Refined 2 Angstroms X-Ray Crystal Structure of Porcine Pancreatic Kallikrein A, a Specific Trypsin-Like Serine Proteinase. Crystallization, Structure Determination,Crystallographic Refinement,Structure and its Comparison with Bovine Trypsin
Authors: Bode, W. / Chen, Z. / Bartels, K. / Kutzbach, C. / Schmidt-Kastner, G. / Bartunik, H.
History
DepositionMay 21, 1984Processing site: BNL
Revision 1.0Jul 19, 1984Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KALLIKREIN A
B: KALLIKREIN A
I: BOVINE PANCREATIC TRYPSIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)32,1583
Polymers32,1583
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-54 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.200, 106.200, 108.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: RESIDUES PRO B 147, PRO B 219, PRO B 246 ARE CIS-PROLINES. ALSO SEE REMARK 5 IF OCCUPANCY IS 0.0.
2: SEE REMARK 5. / 3: SEE REMARK 6.

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Components

#1: Protein KALLIKREIN A


Mass: 9119.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00752, EC: 3.4.21.8
#2: Protein KALLIKREIN A


Mass: 16511.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00752, EC: 3.4.21.8
#3: Protein BOVINE PANCREATIC TRYPSIN INHIBITOR


Mass: 6527.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00974
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.76 Å3/Da / Density % sol: 74.15 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / PH range low: 4.25 / PH range high: 3.75
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.8 Mammonium sulfate1drop
21.2 Mammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 16780 / Observed criterion σ(I): 2 / Num. measured all: 60000 / Rmerge(I) obs: 0.104

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Processing

SoftwareName: EREF / Classification: refinement
RefinementRfactor Rwork: 0.224 / Highest resolution: 2.5 Å
Details: AN OCCUPANCY OF 0.0 INDICATES THAT NO SIGNIFICANT ELECTRON DENSITY WAS FOUND IN THE FINAL FOURIER MAP AND THAT THE COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA. NO COORDINATES ...Details: AN OCCUPANCY OF 0.0 INDICATES THAT NO SIGNIFICANT ELECTRON DENSITY WAS FOUND IN THE FINAL FOURIER MAP AND THAT THE COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA. NO COORDINATES ARE INCLUDED FOR RESIDUE 1 OF PTI OR FOR MOST OF RESIDUE 58 OF PTI. IN ORDER NOT TO RESTRAIN THE APPROACH OF OG OF SER B 195 TO THE SUSCEPTIBLE INHIBITOR BOND, THE NORMAL CONSTRAINTS IMPOSED ON THE NON-BONDED INTERACTIONS BETWEEN THIS ATOM AND THE NEIGHBORING ATOMS OF THE INHIBITOR WERE REMOVED BY CONVERTING THIS OG INTO A NEW ATOM TYPE OI WITH NON-BONDING INTERACTION FORCES OF ZERO. THIS ATOM IS IDENTIFIED AS OG IN THE COORDINATES BELOW.
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 0 10 2247
Refinement
*PLUS
Highest resolution: 2.5 Å / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS

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