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- PDB-8gch: GAMMA-CHYMOTRYPSIN IS A COMPLEX OF ALPHA-CHYMOTRYPSIN WITH ITS OW... -

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Basic information

Entry
Database: PDB / ID: 8gch
TitleGAMMA-CHYMOTRYPSIN IS A COMPLEX OF ALPHA-CHYMOTRYPSIN WITH ITS OWN AUTOLYSIS PRODUCTS
Components
  • (GAMMA-CHYMOTRYPSIN ...) x 3
  • GLY ALA TRP PEPTIDE
KeywordsHYDROLASE/PEPTIDE / HYDROLASE / SERINE PROTEINASE / HYDROLASE-PEPTIDE COMPLEX
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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsHarel, M. / Sussman, J.L. / Silman, I.
CitationJournal: 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.
History
DepositionMar 27, 1991Processing site: BNL
Revision 1.0Apr 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 1.3Jun 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 / Item: _pdbx_entry_details.has_protein_modification

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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
C: GLY ALA TRP PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9798
Polymers25,5954
Non-polymers3844
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-106 kcal/mol
Surface area9740 Å2
MethodPISA
2
E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
C: GLY ALA TRP PEPTIDE
hetero molecules

E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
C: GLY ALA TRP PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,95816
Polymers51,1908
Non-polymers7698
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area19040 Å2
ΔGint-233 kcal/mol
Surface area17340 Å2
MethodPISA
3
E: GAMMA-CHYMOTRYPSIN A

E: GAMMA-CHYMOTRYPSIN A

F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
C: GLY ALA TRP PEPTIDE
hetero molecules

F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
C: GLY ALA TRP PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,95816
Polymers51,1908
Non-polymers7698
Water1448
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 area17370 Å2
ΔGint-220 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.000, 69.000, 95.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Atom site foot note1: SEE REMARK 6.

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Components

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GAMMA-CHYMOTRYPSIN ... , 3 types, 3 molecules EFG

#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

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Protein/peptide , 1 types, 1 molecules C

#4: Protein/peptide GLY ALA TRP PEPTIDE


Mass: 332.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)

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Non-polymers , 2 types, 350 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsREPRESENTED BY CHAINS E, F AND G, THE GAMMA CHYMOTRYPSIN MOLECULE IS COMPRISED OF THREE POLYPEPTIDE ...REPRESENTED BY CHAINS E, F AND G, THE GAMMA CHYMOTRYPSIN MOLECULE IS COMPRISED OF THREE POLYPEPTIDE CHAINS WHICH ARE DERIVED FROM THE ZYMOGEN OF THIS ENZYME BY EXCISION OF RESIDUES 14-15 AND 147-148. RESIDUES 11 THROUGH 13 AND 149 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP AND SO ARE OMITTED. AN ELECTRON DENSITY PEAK IS SEEN ABOUT 1.4 ANGSTROMS FROM THE CARBONYL C ATOM OF RESIDUE LEU 10. THIS PEAK CAN BE ATTRIBUTED EITHER TO A TERMINAL OXYGEN OF A PLANAR CARBONYL GROUP, INDICATING CLEAVAGE OF RESIDUES 11 - 13, OR TO THE N ATOM OF THE FOLLOWING DISORDERED RESIDUE (SER 11). IN THIS ENTRY THE ATOM WAS DENOTED AS OXT LEU 10
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: 2.22 Å3/Da / Density % sol: 44.47 %
Crystal grow
*PLUS
pH: 5.5 / Method: unknown / Details: Cohen, G.H., (1981) J. Mol. Biol., 148, 449.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112.5 mg/mlprotein11
250 %satammonium sulfate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 29204 / Num. measured all: 33900 / Rmerge(I) obs: 0.024

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Processing

RefinementHighest resolution: 1.6 Å
Details: 8GCH RESIDUES GLY 250, ALA 251, AND TRP 252 FORM THE TRIPEPTIDE 8GCH SEEN IN THE ACTIVE SITE. THE TRIPEPTIDE SEQUENCE IS 8GCH DERIVED FROM THE DENSITY SEEN IN THE MAP AND IS REALLY 8GCH THE ...Details: 8GCH RESIDUES GLY 250, ALA 251, AND TRP 252 FORM THE TRIPEPTIDE 8GCH SEEN IN THE ACTIVE SITE. THE TRIPEPTIDE SEQUENCE IS 8GCH DERIVED FROM THE DENSITY SEEN IN THE MAP AND IS REALLY 8GCH THE RESULT OF AN OVERLAP OF DIFFERENT AUTOLYSED 8GCH POLYPEPTIDES BOUND THERE. 8GCH
Refinement stepCycle: LAST / Highest resolution: 1.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 20 346 2131
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 6 Å / σ(I): 1 / Num. reflection obs: 25266 / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.028
X-RAY DIFFRACTIONp_planar_d0.031
X-RAY DIFFRACTIONp_plane_restr0.01
X-RAY DIFFRACTIONp_chiral_restr0.121

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