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- PDB-6gch: STRUCTURE OF CHYMOTRYPSIN-*TRIFLUOROMETHYL KETONE INHIBITOR COMPL... -

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Basic information

Entry
Database: PDB / ID: 6gch
TitleSTRUCTURE OF CHYMOTRYPSIN-*TRIFLUOROMETHYL KETONE INHIBITOR COMPLEXES. COMPARISON OF SLOWLY AND RAPIDLY EQUILIBRATING INHIBITORS
Components(GAMMA-CHYMOTRYPSIN A) x 3
KeywordsHYDROLASE (SERINE PROTEINASE)
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-APF / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsBrady, K. / Wei, A. / Ringe, D. / Abeles, R.H.
Citation
Journal: Biochemistry / Year: 1990
Title: Structure of chymotrypsin-trifluoromethyl ketone inhibitor complexes: comparison of slowly and rapidly equilibrating inhibitors.
Authors: Brady, K. / Wei, A.Z. / Ringe, D. / Abeles, R.H.
#1: 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.
#2: Journal: Biochemistry / Year: 1990
Title: Photolysis and Deacylation of Inhibited Chymotrypsin
Authors: Stoddard, B.L. / Bruhnke, J. / Koenig, P. / Porter, N. / Ringe, D. / Petsko, G.A.
#3: Journal: Biochemistry / Year: 1990
Title: Inhibition of Chymotrypsin by Peptidyl Trifluoromethy Ketones. Determinants of Slow-Binding Kinetics
Authors: Brady, K. / Abeles, R.H.
#4: Journal: Biochemistry / Year: 1989
Title: Ph Dependence of the Inhibition of Chymotrypsin by a Peptidyl Trifluoromethyl Ketone
Authors: Liang, K.Brady.T.-C. / Abeles, R.H.
History
DepositionApr 6, 1990Processing site: BNL
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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
E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5224
Polymers25,2633
Non-polymers2591
Water3,387188
1
E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
hetero molecules

E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0448
Polymers50,5256
Non-polymers5182
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Unit cell
Length a, b, c (Å)69.300, 69.300, 97.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein/peptide GAMMA-CHYMOTRYPSIN A


Mass: 1253.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#2: Protein GAMMA-CHYMOTRYPSIN A


Mass: 13934.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#3: Protein GAMMA-CHYMOTRYPSIN A


Mass: 10074.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#4: Chemical ChemComp-APF / 1,1,1-TRIFLUORO-3-ACETAMIDO-4-PHENYL BUTAN-2-ONE(N-ACETYL-L-PHENYLALANYL TRIFLUOROMETHYL KETONE)


Mass: 259.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12F3NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal grow
*PLUS
pH: 5.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlgamma-chymotrypsin11
210 mMsodium cacodylate11
30.75 %satcetyltrimethylammonium bromide11
444 %satammonium sulfate11
570-75 %satammonium sulfate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / % possible obs: 65 % / Observed criterion σ(I): 1 / Num. measured all: 9225 / Rmerge(I) obs: 0.065

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.1→6 Å
Details: 6GCH PHASES WERE CALCULATED FROM THE MODEL OF G.COHEN ET AL. 6GCH (PROTEIN DATA BANK ENTRY 2GCH) AND APPLIED TO STRUCTURE 6GCH FACTORS COLLATED FROM ALPHA-CHYMOTRYPSIN CRYSTALS WHICH HAD ...Details: 6GCH PHASES WERE CALCULATED FROM THE MODEL OF G.COHEN ET AL. 6GCH (PROTEIN DATA BANK ENTRY 2GCH) AND APPLIED TO STRUCTURE 6GCH FACTORS COLLATED FROM ALPHA-CHYMOTRYPSIN CRYSTALS WHICH HAD 6GCH BEEN SOAKED IN A SOLUTION CONTAINING THE INHIBITOR 6GCH N-ACETYL-L-PHENYLALANYL TRIFLUOROMETHYL KETONE. ALL 6GCH SECONDARY STRUCTURAL FEATURES AND SEQUENCE ARE IDENTICAL TO 6GCH PROTEIN DATA BANK ENTRY 2GCH. 6GCH
RfactorNum. reflection
obs0.18 9255
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 18 188 1944
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0290.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 6 Å / Num. reflection obs: 9255 / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 9.2 Å2

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