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- PDB-1o2u: Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Bindin... -

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Entry
Database: PDB / ID: 1o2u
TitleElaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors
ComponentsBETA-TRYPSIN
KeywordsHYDROLASE / serine protease / short hydrogen bond / inhibition mechanism / shift of pKa / trypsin / thrombin / urokinase / factor Xa
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-847 / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.41 Å
AuthorsKatz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. ...Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W. / Hui, H.C. / Breitenbucher, J.G. / Allen, D. / Janc, J.W.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Elaborate manifold of short hydrogen bond arrays mediating binding of active site-directed serine protease inhibitors.
Authors: Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W. / Hui, H.C. / Breitenbucher, J.G. ...Authors: Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W. / Hui, H.C. / Breitenbucher, J.G. / Allen, D. / Janc, J.W.
History
DepositionMar 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8103
Polymers23,3241
Non-polymers4852
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.85, 61.88, 70.02
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Cell settingorthorhombic
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-847 / 2-(3-{5-[AMINO(IMINIO)METHYL]-1H-BENZIMIDAZOL-2-YL}-5-BROMO-4-OXIDOPHENYL)SUCCINATE / CRA_16847


Mass: 445.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H13BrN4O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.1
Details: sodium citrate soak at target pH (10.34). vapor diffusion at 298 K, pH 8.10

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Data collection

DiffractionMean temperature: 285 K / Ambient temp details: Crystal Cooler
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.41→23.59 Å / Num. all: 54164 / Num. obs: 49944 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 11.5
Reflection shellResolution: 1.41→1.47 Å / % possible obs: 51.3 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 0.9 / Num. unique all: 6659

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Processing

Software
NameVersionClassification
CrystalClear1.3data collection
CrystalClear1.3data reduction
X-PLOR3.851refinement
CrystalClear(MSC/RIGAKU)data scaling
Quantamodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.41→7 Å / Cross valid method: THROUGHOUT / σ(F): 0.5 / Stereochemistry target values: X-PLOR force field
Details: Residues simultaneously refined in two or more conformations are: Val53, Leu66, Ser86, Lys87, Ser110, Ser113, Ser130, Lys159, Asp165, Ser170, Gln175, Ser195, Ser217, Lys230, Ser236, Ser244, ...Details: Residues simultaneously refined in two or more conformations are: Val53, Leu66, Ser86, Lys87, Ser110, Ser113, Ser130, Lys159, Asp165, Ser170, Gln175, Ser195, Ser217, Lys230, Ser236, Ser244, Bzm246 HOH383 makes a short H-bond with 847246 (conf 1). Other H-bonds are normal. His40 and HIS91 are MONOPROTONATED ON THE EPSILON NITROGEN.
RfactorNum. reflection% reflection
Rfree0.207 4861 10 %
Rwork0.196 --
obs0.197 48288 90.02 %
all-53641 -
Refinement stepCycle: LAST / Resolution: 1.41→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 83 411 3854
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_deg3.9

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