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- PDB-1btw: Episelection: novel KI ~nanomolar inhibitors of serine proteases ... -

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Basic information

Entry
Database: PDB / ID: 1btw
TitleEpiselection: novel KI ~nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface
ComponentsBETA-TRYPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / TRIPEPTIDEBORONATE 1 / 3-PROPANEDIOL MONOESTER-INHIBITED / SERINE PROTEINASE / 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
T-BUTOXY-ALA-VAL-BORO-LYS 1,3-PROPANEDIOL MONOESTER / Chem-0ZW / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsStroud, R.M. / Katz, B.A. / Finer-Moore, J.
Citation
Journal: Biochemistry / Year: 1995
Title: Episelection: novel Ki approximately nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface.
Authors: Katz, B.A. / Finer-Moore, J. / Mortezaei, R. / Rich, D.H. / Stroud, R.M.
#1: Journal: Proteins / Year: 1992
Title: Solvent Structure in Crystals of Trypsin Determined by X-Ray and Neutron Diffraction
Authors: Finer-Moore, J.S. / Kossiakoff, A. / Hurley, J.H. / Earnest, T. / Stroud, R.M.
#2: Journal: Proteins / Year: 1991
Title: 1.59 Angstrom Structure of Trypsin at 120K: Comparison of Low Temperature and Room Temperature Structures
Authors: Earnest, T. / Fauman, E. / Craik, C.S. / Stroud, R.M.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1977
Title: Difference Fourier Refinement of the Structure of Dip-Trypsin at 1.5 Angstroms Using a Minicomputer Technique
Authors: Chambers, J.L. / Stroud, R.M.
#4: Journal: J.Mol.Biol. / Year: 1974
Title: Structure and Specific Binding of Trypsin, Comparison of Inhibited Derivatives and a Model for Substrate Binding
Authors: Krieger, M. / Kay, L.M. / Stroud, R.M.
#5: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: The Crystal and Molecular Structure of Dip-Inhibited Bovine Trypsin at 2.7 Angstroms Resolution
Authors: Stroud, R.M. / Kay, L.M. / Dickerson, R.E.
History
DepositionMay 17, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 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 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: 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: BETA-TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5283
Polymers24,0131
Non-polymers5152
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.740, 63.540, 68.930
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 BETA-TRYPSIN


Mass: 24012.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-0ZW / N-(tert-butoxycarbonyl)-L-alanyl-N-{(1S)-5-ammonio-1-[hydroxy(3-hydroxypropoxy)boranyl]pentyl}-L-valinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 475.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44BN4O7
References: T-BUTOXY-ALA-VAL-BORO-LYS 1,3-PROPANEDIOL MONOESTER
#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.: 172 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE INHIBITOR WAS SYNTHESIZED AS THE PINANEDIOL DIESTER P-TOLUENESULFONATE SALT. THE PROPANEDIOL ...THE INHIBITOR WAS SYNTHESIZED AS THE PINANEDIOL DIESTER P-TOLUENESULFONATE SALT. THE PROPANEDIOL ESTER SEEN IN THE CRYSTAL STRUCTURE WAS OBTAINED BY INCUBATING TRYPSIN WITH THE T-BUTOXY-ALA-VAL-BOROLYS-C10H16 PARA-TOLUENESULFONIC ACID IN THE PRESENCE OF ETHANOL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used seeding

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Data collection

RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 15938 / % possible obs: 50.6 % / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 7 Å

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Processing

Software
NameVersionClassification
RAXISIIC PROGRAMSdata collection
X-PLORmodel building
X-PLORrefinement
R-AXISIICdata reduction
X-PLORphasing
RefinementResolution: 1.7→7 Å / σ(F): 3.3 /
RfactorNum. reflection
Rwork0.164 -
obs0.164 12248
Refinement stepCycle: LAST / Resolution: 1.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 34 172 1835
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.3
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
Highest resolution: 1.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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