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- PDB-3gch: CHEMISTRY OF CAGED ENZYMES. BINDING OF PHOTOREVERSIBLE CINNAMATES... -

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Basic information

Entry
Database: PDB / ID: 3gch
TitleCHEMISTRY OF CAGED ENZYMES. BINDING OF PHOTOREVERSIBLE CINNAMATES TO CHYMOTRYPSIN
Components(GAMMA-CHYMOTRYPSIN) 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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
TRANS-O-HYDROXY-ALPHA-METHYL CINNAMATE / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (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 Trifluoromethyl 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: Brady, K. / Liang, T.-C. / Abeles, R.H.
History
DepositionSep 25, 1989-
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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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)25,4434
Polymers25,2633
Non-polymers1801
Water1,36976
1
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)50,8868
Polymers50,5256
Non-polymers3602
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 area6940 Å2
ΔGint-57 kcal/mol
Surface area9960 Å2
MethodPISA
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


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


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


Mass: 10074.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#4: Chemical ChemComp-OAC / TRANS-O-HYDROXY-ALPHA-METHYL CINNAMATE


Mass: 180.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlchymotorypsin1drop
210 mMsodium cacodylate1drop
30.75 %satcetyltrimethylammonium bromide1drop
445 %satammonium sulfate1drop
565 %satammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Num. obs: 9635 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.05

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→50 Å /
RfactorNum. reflection
obs0.203 9635
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 12 76 1824
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
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_restr0.2210.15
X-RAY DIFFRACTIONp_singtor_nbd0.2150.5
X-RAY DIFFRACTIONp_multtor_nbd0.3090.5
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
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
σ(I): 2 / Rfactor obs: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS

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