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- PDB-1jrs: HEMIACETAL COMPLEX BETWEEN LEUPEPTIN AND TRYPSIN -

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Basic information

Entry
Database: PDB / ID: 1jrs
TitleHEMIACETAL COMPLEX BETWEEN LEUPEPTIN AND TRYPSIN
Components
  • Leupeptin
  • TRYPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / SERINE PROTEASE / DIGESTION / PANCREAS / ZYMOGEN / HYDROLASE (SERINE PROTEASE) / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


trypsin / serpin family protein binding / digestion / serine protease inhibitor complex / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
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. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...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. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / 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
LEUPEPTIN / : / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
Actinomycetes Streptomyces roseus MA 839-A1 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsKurinov, I.V. / Harrison, R.W.
Citation
Journal: Protein Sci. / Year: 1996
Title: Two crystal structures of the leupeptin-trypsin complex.
Authors: Kurinov, I.V. / Harrison, R.W.
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: Prediction of New Serine Proteinase Inhibitors
Authors: Kurinov, I.V. / Harrison, R.W.
History
DepositionFeb 7, 1996-
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN
B: Leupeptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7943
Polymers23,7542
Non-polymers401
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-16 kcal/mol
Surface area8860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.686, 69.373, 63.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRYPSIN /


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Protein/peptide Leupeptin / /


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 429.578 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Actinomycetes Streptomyces roseus MA 839-A1 (bacteria)
References: NOR: NOR00487, LEUPEPTIN, trypsin
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE LEUPEPTIN IS COVALENTLY CONNECTED TO ACTIVE_SITE SER 195 OF THE ENZYME TO FORM A HEMIACETAL.
Sequence detailsTHERE IS A DISCREPANCY IN THE NORINE AND PDB NUMBERING, AS NORINE COUNTS ACE AND LEU TOGETHER AS ...THERE IS A DISCREPANCY IN THE NORINE AND PDB NUMBERING, AS NORINE COUNTS ACE AND LEU TOGETHER AS ONE RESIDUE. SO THE DBREF WILL REPORT 4 PDB RESIDUES MATCHING NORINE 3 RESIDUE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 56 %
Crystal growMethod: vapor diffusion, hanging drop
Details: ORTHORHOMBIC SPACE GROUP; CRYSTALLIZATION CONDITIONS: 24-26% PEG8000, 0.02M INHIBITOR, 0.2M (NH4)2 SO4, 50MM TRIS-HCL, ROOM TEMPERATURE, HANGING DROP., vapor diffusion - hanging drop
Temp details: room temp
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130-40 mg/mlprotein1drop
224-26 %PEG80001reservoir
30.02 Minhibitor1reservoir
40.2 Mammonium sulfate1reservoir
550 mMTris-HCl1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 19, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 78707 / % possible obs: 88.8 % / Observed criterion σ(I): 1 / Redundancy: 3.24 % / Rmerge(I) obs: 0.044
Reflection
*PLUS
Highest resolution: 1.8 Å

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Processing

Software
NameVersionClassification
PROCESSdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
PROCESSdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.8→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.207 -
Rwork0.175 -
obs0.175 23223
Displacement parametersBiso mean: 22.2 Å2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 1 170 1830
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.6
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
Solvent computation
*PLUS
Displacement parameters
*PLUS

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