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- PDB-2gmt: THREE-DIMENSIONAL STRUCTURE OF CHYMOTRYPSIN INACTIVATED WITH (2S)... -

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Basic information

Entry
Database: PDB / ID: 2gmt
TitleTHREE-DIMENSIONAL STRUCTURE OF CHYMOTRYPSIN INACTIVATED WITH (2S) N-ACETYL-L-ALANYL-L-PHENYLALANYL-CHLOROETHYL KETONE: IMPLICATIONS FOR THE MECHANISM OF INACTIVATION OF SERINE PROTEASES BY CHLOROKETONES
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 / 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-HIN / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsKreutter, K. / Steinmetz, A.C.U. / Liang, T.-C. / Prorok, M. / Abeles, R. / Ringe, D.
CitationJournal: Biochemistry / Year: 1994
Title: Three-dimensional structure of chymotrypsin inactivated with (2S)-N-acetyl-L-alanyl-L-phenylalanyl alpha-chloroethane: implications for the mechanism of inactivation of serine proteases by chloroketones.
Authors: Kreutter, K. / Steinmetz, A.C. / Liang, T.C. / Prorok, M. / Abeles, R.H. / Ringe, D.
History
DepositionSep 7, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 7, 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_conn / struct_sheet / 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_sheet.number_strands / _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
A: GAMMA-CHYMOTRYPSIN
B: GAMMA-CHYMOTRYPSIN
C: GAMMA-CHYMOTRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5874
Polymers25,2633
Non-polymers3251
Water4,288238
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)51,1758
Polymers50,5256
Non-polymers6502
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area17480 Å2
ΔGint-103 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.500, 69.500, 97.600
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 genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#2: Protein GAMMA-CHYMOTRYPSIN


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


Mass: 10074.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / References: UniProt: P00766, chymotrypsin
#4: Chemical ChemComp-HIN / (2S) N-ACETYL-L-ALANYL-ALPHAL-PHENYLALANYL-CHLOROETHYLKETONE


Mass: 324.803 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21ClN2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 47.49 %
Crystal grow
*PLUS
Method: unknown

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Num. obs: 13167 / % possible obs: 91 % / Num. measured all: 20852 / Rmerge F obs: 0.042

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.8→20 Å /
RfactorNum. reflection
obs0.188 13167
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 21 238 1995
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_deg3
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_d33
X-RAY DIFFRACTIONt_plane_restr0.020.02

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