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- PDB-4gch: STRUCTURE AND ACTIVITY OF TWO PHOTOREVERSIBLE CINNAMATES BOUND TO... -

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Basic information

Entry
Database: PDB / ID: 4gch
TitleSTRUCTURE AND ACTIVITY OF TWO PHOTOREVERSIBLE CINNAMATES BOUND TO CHYMOTRYPSIN
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-DMC / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsStoddard, B.L. / Ringe, D. / Petsko, G.A.
Citation
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.
#1: 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.
#2: Journal: Biochemistry / Year: 1990
Title: Structure of Chymotrypsin-Trifluoromethyl Ketone Inhibitor Complexes. Comparison of Slowly and Rapidly Equilibrating Inhibitors
Authors: Brady, K. / Wei, A. / Ringe, D. / Abeles, R.H.
#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
DepositionSep 25, 1989Processing site: BNL
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: 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
E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5124
Polymers25,2633
Non-polymers2491
Water1,31573
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)51,0248
Polymers50,5256
Non-polymers4992
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-55 kcal/mol
Surface area9980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.700, 69.700, 97.500
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-DMC / 3-(4-DIETHYLAMINO-2-HYDROXY-PHENYL)-2-METHYL-PROPIONIC ACID / PARA-DIETHYLAMINO-O-HYDROXY-ALPHA-METHYL CINNAMIC ACID


Mass: 249.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal grow
*PLUS
pH: 5.6 / Method: other
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

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 10856 / Rmerge(I) obs: 0.052

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→45 Å /
RfactorNum. reflection
obs0.209 10856
Refinement stepCycle: LAST / Resolution: 1.9→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 17 73 1826
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0260.025
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_restr0.2380.15
X-RAY DIFFRACTIONp_singtor_nbd0.2370.5
X-RAY DIFFRACTIONp_multtor_nbd0.3150.5
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
σ(I): 2 / Highest resolution: 1.9 Å / Lowest resolution: 45 Å / Num. reflection obs: 10856 / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS

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