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- PDB-1qa0: BOVINE TRYPSIN 2-AMINOBENZIMIDAZOLE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1qa0
TitleBOVINE TRYPSIN 2-AMINOBENZIMIDAZOLE COMPLEX
ComponentsTRYPSIN
KeywordsHYDROLASE / PROTEIN-INHIBITOR COMPLEX / S1 POCKET / SERINE PROTEASE
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
1H-benzimidazol-2-amine / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsWhitlow, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallographic analysis of potent and selective factor Xa inhibitors complexed to bovine trypsin.
Authors: Whitlow, M. / Arnaiz, D.O. / Buckman, B.O. / Davey, D.D. / Griedel, B. / Guilford, W.J. / Koovakkat, S.K. / Liang, A. / Mohan, R. / Phillips, G.B. / Seto, M. / Shaw, K.J. / Xu, W. / Zhao, Z. ...Authors: Whitlow, M. / Arnaiz, D.O. / Buckman, B.O. / Davey, D.D. / Griedel, B. / Guilford, W.J. / Koovakkat, S.K. / Liang, A. / Mohan, R. / Phillips, G.B. / Seto, M. / Shaw, K.J. / Xu, W. / Zhao, Z. / Light, D.R. / Morrissey, M.M.
#1: Journal: FEBS Lett. / Year: 1978
Title: Crystal Structure Analysis and Refinement of Two Variants of Trigonal Trypsinogen
Authors: Bode, W. / Huber, R.
#2: Journal: Methods (San Diego) / Year: 1990
Title: ANALYTICAL AND PRODUCTION SEEDING TECHNIQUES
Authors: Stura, E.A. / Wilson, I.A.
History
DepositionApr 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_src_syn / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _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 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 2.0Aug 13, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4983
Polymers23,3241
Non-polymers1732
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.02, 55.02, 109.14
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

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Components

#1: Protein TRYPSIN / E.C.3.4.21.4


Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: BOVINE TRYPSIN / Mutation: NONE / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: BOVINE 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 / Details: BOEHRINGER MANNHEIM CORP. 109,827, ALRICH 17,177-8
#3: Chemical ChemComp-AX7 / 1H-benzimidazol-2-amine


Mass: 133.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7N3 / Details: SIGMA C 5080
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.04 Å3/Da / Density % sol: 39.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: MICROCRYSTALS WERE INITIALLY GROWN USING THE HANGING DROP METHOD IN LINBRO CULTURE PLATES. CRYSTALLIZATION RESERVOIRS CONTAIN 1.8 - 2.0 M AMMONIUM SULFATE, 50 MM TRIS HCL, 10 MM CACL2, PH 7. ...Details: MICROCRYSTALS WERE INITIALLY GROWN USING THE HANGING DROP METHOD IN LINBRO CULTURE PLATES. CRYSTALLIZATION RESERVOIRS CONTAIN 1.8 - 2.0 M AMMONIUM SULFATE, 50 MM TRIS HCL, 10 MM CACL2, PH 7.4. SIX UL OF 15 MG/ML BOVINE TRYPSIN IN 20 MM 2-AMINOBENZIMIDAZOLE WAS ADDED TO 6 UL OF RESERVOIR. MACROSEEDING WAS USED TO GROW LARGE CRYSTALS (REF 2). SINGLE CRYSTALS WERE WASHED IN 0.8 M AMMONIUM SULFATE, 50 MM TRIS HCL, 10 MM CACL2, PH 7.4. THE WASHED CRYSTALS WERE PLACED IN A 18 HOUR OLD HANGING., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.8-2.0 Mammonium sulfate1reservoir
250 mMTris-HCl1reservoir
310 mM1reservoirCaCl2
415 mg/mltrypsin1drop
520 mM2-aminobenzimidazole1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 10, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. all: 16893 / Num. obs: 16893 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.022 / % possible all: 78.5
Reflection
*PLUS
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 78.5 % / Rmerge(I) obs: 0.0262 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
PROFFTrefinement
XTALVIEWrefinement
SCALEPACKdata scaling
RefinementResolution: 1.8→10 Å / σ(F): 2 / Details: USED RESTRAINED LEAST SQUARES /
RfactorNum. reflection
Rwork0.172 -
obs0.172 16656
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 11 125 1765
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0330.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.0082
X-RAY DIFFRACTIONp_mcangle_it2.5683
X-RAY DIFFRACTIONp_scbond_it3.6053
X-RAY DIFFRACTIONp_scangle_it4.6694
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.1670.15
X-RAY DIFFRACTIONp_singtor_nbd0.1670.5
X-RAY DIFFRACTIONp_multtor_nbd0.1850.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2030.5
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor17.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor18.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_mcbond_it2
X-RAY DIFFRACTIONp_scbond_it3
X-RAY DIFFRACTIONp_mcangle_it3
X-RAY DIFFRACTIONp_scangle_it4

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