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- PDB-1ghb: A SECOND ACTIVE SITE IN CHYMOTRYPSIN? THE X-RAY CRYSTAL STRUCTURE... -

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Basic information

Entry
Database: PDB / ID: 1ghb
TitleA SECOND ACTIVE SITE IN CHYMOTRYPSIN? THE X-RAY CRYSTAL STRUCTURE OF N-ACETYL-D-TRYPTOPHAN BOUND TO GAMMA-CHYMOTRYPSIN
Components
  • (GAMMA-CHYMOTRYPSIN) x 3
  • PRO-GLY-ALA
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR 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
ACETYL GROUP / HEXANE / ISOPROPYL ALCOHOL / TRYPTOPHAN / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsYennawar, H.P. / Yennawar, N.H. / Farber, G.K.
Citation
Journal: J.Am.Chem.Soc. / Year: 1995
Title: A STRUCTURAL EXPLANATION FOR ENZYME MEMORY IN NONAQUEOUS SOLVENTS.
Authors: Yennawar, H.P. / Yennawar, N.H. / Farber, G.K.
#1: Journal: To be Published
Title: X-Ray Crystal Structure of Gamma-Chymotrypsin in Hexane
Authors: Yennawar, N.H. / Yennawar, H.P. / Farber, G.K.
History
DepositionApr 6, 1994Processing site: BNL
Revision 1.0Jun 22, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 6, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: GAMMA-CHYMOTRYPSIN
F: GAMMA-CHYMOTRYPSIN
G: GAMMA-CHYMOTRYPSIN
P: PRO-GLY-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,36514
Polymers25,5064
Non-polymers85910
Water5,567309
1
E: GAMMA-CHYMOTRYPSIN
F: GAMMA-CHYMOTRYPSIN
G: GAMMA-CHYMOTRYPSIN
P: PRO-GLY-ALA
hetero molecules

E: GAMMA-CHYMOTRYPSIN
F: GAMMA-CHYMOTRYPSIN
G: GAMMA-CHYMOTRYPSIN
P: PRO-GLY-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,73128
Polymers51,0128
Non-polymers1,71920
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
2
E: GAMMA-CHYMOTRYPSIN
hetero molecules

E: GAMMA-CHYMOTRYPSIN
hetero molecules

F: GAMMA-CHYMOTRYPSIN
G: GAMMA-CHYMOTRYPSIN
P: PRO-GLY-ALA
hetero molecules

F: GAMMA-CHYMOTRYPSIN
G: GAMMA-CHYMOTRYPSIN
P: PRO-GLY-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,73128
Polymers51,0128
Non-polymers1,71920
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_785-x+2,-y+3,z1
crystal symmetry operation5_656-x+3/2,y+1/2,-z+3/21
crystal symmetry operation6_576x+1/2,-y+5/2,-z+3/21
Buried area17470 Å2
ΔGint-60 kcal/mol
Surface area22320 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.600, 69.600, 97.510
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 , 2 types, 2 molecules EP

#1: Protein/peptide GAMMA-CHYMOTRYPSIN


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
#4: Protein/peptide PRO-GLY-ALA


Mass: 243.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

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Protein , 2 types, 2 molecules FG

#2: Protein GAMMA-CHYMOTRYPSIN


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


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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Non-polymers , 5 types, 319 molecules

#5: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#6: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#7: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14
#8: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal grow
*PLUS
pH: 5.6 / Method: batch method / Details: Yennawar, N. H., (1994) Biochemistry, 33, 7326.
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 sulphate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 15361 / Rmerge(I) obs: 0.14

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.152 / Rfactor obs: 0.152 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1754 0 60 309 2123
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_deg1.606
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 5 Å / Rfactor obs: 0.152 / Rfactor Rwork: 0.152 / Highest resolution: 2.2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.606

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