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- PDB-2vgc: GAMMA-CHYMOTRYPSIN D-PARA-CHLORO-1-ACETAMIDO BORONIC ACID INHIBIT... -

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Basic information

Entry
Database: PDB / ID: 2vgc
TitleGAMMA-CHYMOTRYPSIN D-PARA-CHLORO-1-ACETAMIDO BORONIC ACID INHIBITOR COMPLEX
Components(GAMMA CHYMOTRYPSIN) x 3
KeywordsSERINE PROTEASE / HYDROLASE
Function / homology
Function and homology information


chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase activity / proteolysis / extracellular region
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 / Trypsin-like serine proteases ...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-V35 / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / DIRECT SOLUTION WITH KNOWN STRUCTURE / Resolution: 1.8 Å
AuthorsStoll, V.S. / Eger, B.T. / Hynes, R.C. / Martichonok, V. / Jones, J.B. / Pai, E.F.
Citation
Journal: Biochemistry / Year: 1998
Title: Differences in binding modes of enantiomers of 1-acetamido boronic acid based protease inhibitors: crystal structures of gamma-chymotrypsin and subtilisin Carlsberg complexes.
Authors: Stoll, V.S. / Eger, B.T. / Hynes, R.C. / Martichonok, V. / Jones, J.B. / Pai, E.F.
#1: Journal: J.Am.Chem.Soc. / Year: 1996
Title: Probing the Specificity of the Serine Proteases Subtilisin Carlsberg and A-Chymotrypsin with Enantiomeric 1-Acetamido Boronic Acids. An Unexpected Reversal of the Normal
Authors: Martichonok, V. / Jones, J.B.
#2: Journal: Bioorg.Med.Chem. / Year: 1994
Title: Probing the Specificity of the S1 Binding Site of Subtilisin Carlsberg with Boronic Acids
Authors: Seufer-Wasserthal, P. / Martichonok, V. / Keller, T.H. / Chin, B. / Martin, R. / Jones, J.B.
#3: Journal: Biochemistry / Year: 1991
Title: Gamma-Chymotrypsin is a Complex of Alpha-Chymotrypsin with its Own Autolysis Products
Authors: Harel, M. / Su, C.T. / Frolow, F. / Silman, I. / Sussman, J.L.
#4: Journal: Biochemistry / Year: 1990
Title: Structure and Activity of Two Photoreversible Cinnamates Bound to Chymotrypsin
Authors: Stoddard, B.L. / Bruhnke, J. / Porter, N. / Ringe, D. / Petsko, G.A.
History
DepositionMay 1, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: GAMMA CHYMOTRYPSIN
B: GAMMA CHYMOTRYPSIN
C: GAMMA CHYMOTRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7136
Polymers25,2633
Non-polymers4513
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-86 kcal/mol
Surface area9750 Å2
MethodPISA
2
A: GAMMA CHYMOTRYPSIN
B: GAMMA CHYMOTRYPSIN
C: GAMMA CHYMOTRYPSIN
hetero molecules

A: GAMMA CHYMOTRYPSIN
B: GAMMA CHYMOTRYPSIN
C: GAMMA CHYMOTRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,42612
Polymers50,5256
Non-polymers9016
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area17990 Å2
ΔGint-187 kcal/mol
Surface area17330 Å2
MethodPISA
3
A: GAMMA CHYMOTRYPSIN

A: GAMMA CHYMOTRYPSIN

B: GAMMA CHYMOTRYPSIN
C: GAMMA CHYMOTRYPSIN
hetero molecules

B: GAMMA CHYMOTRYPSIN
C: GAMMA CHYMOTRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,42612
Polymers50,5256
Non-polymers9016
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation5_545-x+1/2,y-1/2,-z+1/21
crystal symmetry operation6_555x+1/2,-y+1/2,-z+1/21
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area16470 Å2
ΔGint-173 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.689, 69.689, 96.787
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide GAMMA CHYMOTRYPSIN


Mass: 1253.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: A-CHYMOTRYPSIN PURCHASED FROM SIGMA AND CONVERTED TO G-CHYMOTRYPSIN BY THE METHOD OF STODDARD ET AL., 1990, BIOCHEMISTRY, VOL. 29, P. 4871-4879
Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin

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Protein , 2 types, 2 molecules BC

#2: Protein GAMMA CHYMOTRYPSIN


Mass: 13934.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: A-CHYMOTRYPSIN PURCHASED FROM SIGMA AND CONVERTED TO G-CHYMOTRYPSIN BY THE METHOD OF STODDARD ET AL., 1990, BIOCHEMISTRY, VOL. 29, P. 4871-4879
Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin
#3: Protein GAMMA CHYMOTRYPSIN


Mass: 10074.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: A-CHYMOTRYPSIN PURCHASED FROM SIGMA AND CONVERTED TO G-CHYMOTRYPSIN BY THE METHOD OF STODDARD ET AL., 1990, BIOCHEMISTRY, VOL. 29, P. 4871-4879
Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin

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Non-polymers , 3 types, 98 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-V35 / D-1-(4-CHLOROPHENYL)-2-(ACETAMIDO)ETHANE BORONIC ACID / D-PARA-CHLORO-1-ACETAMIDO BORONIC ACID


Mass: 258.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14BClNO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED IN SCINTILLATION VIALS IN 65% AMMONIUM SULFATE, 100 MM CACODYLATE, PH 6.5
Crystal grow
*PLUS
Details: Stoddard, B.L., (1990) Biochemistry, 29, 4871.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlchymotrypsin11
210 mMsodium cacodylate11
30.75 %satcetyltrimethylammonium bromide11
445 %satammonium sulfate11
565 %satammonium sulfate12

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1995 / Details: FRANKS MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 22354 / % possible obs: 79.69 % / Observed criterion σ(I): 1 / Redundancy: 3.47 % / Rsym value: 0.082
Reflection shellResolution: 1.8→1.88 Å / Rsym value: 0.241 / % possible all: 56.49
Reflection
*PLUS
% possible obs: 88.4 % / Rmerge(I) obs: 0.082

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: DIRECT SOLUTION WITH KNOWN STRUCTURE
Starting model: PDB ENTRY 3GCH

3gch


Resolution: 1.8→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1944 8.8 %RANDOM
Rwork0.2103 ---
obs0.2103 16276 79.58 %-
Refine analyzeLuzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 36 88 2570
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.688
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.82
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.436
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
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.308 163 6.7 %
Rwork0.2673 1565 -
obs--56.49 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDXV35.HISTOPHCSDXV35.HIS
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.PEP
X-RAY DIFFRACTION3PAR.SULTOP.SUL
X-RAY DIFFRACTION4TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2542
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.82
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.436

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