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- PDB-1zzz: Trypsin inhibitors with rigid tripeptidyl aldehydes -

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Basic information

Entry
Database: PDB / ID: 1zzz
TitleTrypsin inhibitors with rigid tripeptidyl aldehydes
ComponentsTRYPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR complex
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
N-(benzylsulfonyl)-L-norvalyl-N-{(1R)-2-[(3R)-1-carbamimidoylpiperidin-3-yl]-1-formylethyl}glycinamide / Chem-0IV / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKrishnan, R. / Zhang, E. / Hakansson, K. / Arni, R.K. / Tulinsky, A. / Lim-Wilby, M.S.L. / Levy, O.E. / Semple, J.E. / Brunck, T.K.
CitationJournal: Biochemistry / Year: 1998
Title: Highly selective mechanism-based thrombin inhibitors: structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes.
Authors: Krishnan, R. / Zhang, E. / Hakansson, K. / Arni, R.K. / Tulinsky, A. / Lim-Wilby, M.S. / Levy, O.E. / Semple, J.E. / Brunck, T.K.
History
DepositionJun 2, 1998Processing site: BNL
Revision 1.0Jun 15, 1999Provider: 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
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.process_site / _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: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)25,2873
Polymers24,7401
Non-polymers5472
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.670, 63.200, 69.220
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 / TRP-CVS1694


Mass: 24739.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00760
#2: Chemical ChemComp-0IV / 2-{(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}-N-{(2S)-1-[(3R)-1-carbamimidoylpiperidin-3-yl]-3-oxopropan-2-yl}acetamide / CVS1694


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 506.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H34N6O5S
References: N-(benzylsulfonyl)-L-norvalyl-N-{(1R)-2-[(3R)-1-carbamimidoylpiperidin-3-yl]-1-formylethyl}glycinamide
#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


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE ACTIVE SITE INHIBITOR IS IN ITS R CHIRAL FORM. THE ACTIVE SITE SER 195 IS CLOSE TO THE CARBONYL ...THE ACTIVE SITE INHIBITOR IS IN ITS R CHIRAL FORM. THE ACTIVE SITE SER 195 IS CLOSE TO THE CARBONYL CARBON (C9) OF THE ALDEHYDE GROUP OF THE INHIBITOR FORMING A TRANSITION-STATE COMPLEX.

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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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
21.0 Mbenzamidine1drop
31.9 Mammonium sulfate1drop
40.1 MTris-HCl1drop
50.01 M1dropCaCl2
61.9 Mammonium sulfate1reservoir
70.1 MTris-HCl1reservoir
80.01 M1reservoirCaCl2

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1995
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 16355 / % possible obs: 72 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.043 / Rsym value: 0.12 / Net I/σ(I): 15.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.25 / % possible all: 43
Reflection
*PLUS
Redundancy: 2.5 % / Num. measured all: 41525
Reflection shell
*PLUS
% possible obs: 43 % / Rmerge(I) obs: 0.103

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Processing

Software
NameVersionClassification
RIGAKUSOFTWAREdata collection
RIGAKUSOFTWAREdata reduction
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
RIGAKUdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPC

1ppc


Resolution: 1.9→7 Å / Cross valid method: THROUGHOUT / σ(F): 4
RfactorNum. reflection% reflection
Rwork0.157 --
obs-15565 72 %
Displacement parametersBiso mean: 20.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 7 Å
Refinement stepCycle: LAST / Resolution: 1.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 29 157 1815
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0350.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0550.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.11
X-RAY DIFFRACTIONp_mcangle_it1.81.5
X-RAY DIFFRACTIONp_scbond_it2.62
X-RAY DIFFRACTIONp_scangle_it3.82.5
X-RAY DIFFRACTIONp_plane_restr0.0270.03
X-RAY DIFFRACTIONp_chiral_restr0.150.2
X-RAY DIFFRACTIONp_singtor_nbd0.220.6
X-RAY DIFFRACTIONp_multtor_nbd0.310.6
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.280.6
X-RAY DIFFRACTIONp_planar_tor43
X-RAY DIFFRACTIONp_staggered_tor2015
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor3020
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 9 Å / Rfactor obs: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS

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