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- PDB-1gi3: A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTER... -

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Basic information

Entry
Database: PDB / ID: 1gi3
TitleA NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE
ComponentsBETA-TRYPSIN
KeywordsHYDROLASE / three-centered / very short hydrogen bond / oxyanion hole water / shift of pKa of His57 / structure-based drug design / specificity / urokinase / trypsin / thrombin / Zn+2-mediated inhibition
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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
Chem-BMZ / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.44 Å
AuthorsKatz, B.A. / Elrod, K. / Luong, C. / Rice, M. / Mackman, R.L. / Sprengeler, P.A. / Spencer, J. / Hatayte, J. / Janc, J. / Link, J. ...Katz, B.A. / Elrod, K. / Luong, C. / Rice, M. / Mackman, R.L. / Sprengeler, P.A. / Spencer, J. / Hatayte, J. / Janc, J. / Link, J. / Litvak, J. / Rai, R. / Rice, K. / Sideris, S. / Verner, E. / Young, W.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site.
Authors: Katz, B.A. / Elrod, K. / Luong, C. / Rice, M.J. / Mackman, R.L. / Sprengeler, P.A. / Spencer, J. / Hataye, J. / Janc, J. / Link, J. / Litvak, J. / Rai, R. / Rice, K. / Sideris, S. / Verner, E. / Young, W.
History
DepositionJan 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6183
Polymers23,3241
Non-polymers2932
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.90, 62.27, 70.08
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BETA-TRYPSIN / E.C.3.4.21.4


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BMZ / 2-(2-HYDROXY-PHENYL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE


Mass: 253.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.1
Details: magnesium sulfate soak at pH 9.52. vapor diffusion at 298 K, pH 8.10
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 8.2 / PH range high: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
20.10 MHEPES1reservoirpH7.5 or 8.2
30.30 M1reservoirNaCl
422 %(v/v)PEG5000 MME1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 18, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.32→47.22 Å / Num. all: 65870 / Num. obs: 40323 / % possible obs: 61.2 % / Observed criterion σ(I): 0.8 / Redundancy: 3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.4
Reflection shellResolution: 1.44→1.51 Å / Rmerge(I) obs: 0.255 / Num. unique all: 2334 / % possible all: 37.2
Reflection
*PLUS
Num. measured all: 110074

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Processing

Software
NameVersionClassification
bioteXdata collection
bioteXdata reduction
X-PLOR3.851refinement
bioteXdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.44→7.5 Å / σ(F): 1.8 / Stereochemistry target values: X-PLOR force field
Details: Residues simultaneously refined in two or more conformations are: Val53, Leu66, Ser86, Ser113, Ser130, Lys159, Asp165, Ser170, Ser217, Lys230, Ser236 Note that HOH383 makes short H-bonds to ...Details: Residues simultaneously refined in two or more conformations are: Val53, Leu66, Ser86, Ser113, Ser130, Lys159, Asp165, Ser170, Ser217, Lys230, Ser236 Note that HOH383 makes short H-bonds to OgSer195 and O6' of the inhibitor Disordered waters are: HOH304 which is close to HOH305; HOH331 which is close to HOH332; HOH398 which is close to HOH399; HOH407 which is close to HOH408 which is close to HOH409; HOH468 which is close to HOH469 which is close to HOH470; HOH537 which is close to HOH538; HOH618 which is close to HOH619; HOH719 which is close to HOH720 which is close to HOH721; HOH838 which is close to HOH839; HOH917 which is close to HOH918; His40 and HIS91 are MONOPROTONATED ON THE EPSILON NITROGEN. His57 is doubly protonated.
RfactorNum. reflection% reflection
Rfree0.235 3640 10 %
Rwork0.202 --
obs0.206 35750 70 %
all-51071 -
Refinement stepCycle: LAST / Resolution: 1.44→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 32 825 4169
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_deg3.6
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 7.5 Å / σ(F): 1.8 / % reflection Rfree: 10 % / Rfactor all: 0.206 / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg3.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.4
LS refinement shell
*PLUS
Highest resolution: 1.44 Å / Lowest resolution: 1.51 Å / Rfactor Rfree: 0.235 / Rfactor obs: 0.206

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