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- PDB-6cha: STRUCTURE OF A TETRAHEDRAL TRANSITION STATE COMPLEX OF ALPHA-*CHY... -

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Basic information

Entry
Database: PDB / ID: 6cha
TitleSTRUCTURE OF A TETRAHEDRAL TRANSITION STATE COMPLEX OF ALPHA-*CHYMOTRYPSIN AT 1.8-*ANGSTROMS RESOLUTION
Components(ALPHA-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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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
PHENYLETHANE BORONIC ACID / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsTulinsky, A. / Blevins, R.A.
Citation
Journal: J.Biol.Chem. / Year: 1987
Title: Structure of a tetrahedral transition state complex of alpha-chymotrypsin dimer at 1.8-A resolution.
Authors: Tulinsky, A. / Blevins, R.A.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1986
Title: Least-Squares Refinement of Two Protein Molecules Per Asymmetric Unit with and without Non-Crystallographic Symmetry Restrained
Authors: Tulinsky, A. / Blevins, R.A.
#2: Journal: J.Biol.Chem. / Year: 1985
Title: The Refinement and the Structure of the Dimer of Alpha-Chymotrypsin at 1.67-Angstroms Resolution
Authors: Blevins, R.A. / Tulinsky, A.
#3: Journal: J.Biol.Chem. / Year: 1985
Title: Comparison of the Independent Solvent Structures of Dimeric Alpha-Chymotrypsin with Themselves and with Gamma-Chymotrypsin
Authors: Blevins, R.A. / Tulinsky, A.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1979
Title: The Structure of Alpha-Chymotrypsin. II. Fourier Phase Refinement and Extension of the Dimeric Modification
Authors: Raghavan, N.V. / Tulinsky, A.
#5: Journal: Acta Crystallogr.,Sect.B / Year: 1973
Title: The Structure of Alpha-Chymotrypsin. I. The Refinement of the Heavy-Atom Isomorphous Derivatives at 2.8 Angstroms Resolution
Authors: Tulinsky, A. / Mani, N.V. / Morimoto, C.N. / Vandlen, R.L.
#6: Journal: Biochemistry / Year: 1973
Title: Variability in the Tertiary Structure of Alpha-Chymotrypsin at 2.8-Angstroms Resolution
Authors: Tulinsky, A. / Vandlen, R.L. / Morimoto, C.N. / Mani, N.V. / Wright, L.H.
#7: Journal: Biochemistry / Year: 1974
Title: Asymmetrical Changes in the Tertiary Structure of Alpha-Chymotrypsin with Change in Ph
Authors: Mavridis, A. / Tulinsky, A. / Liebman, M.N.
History
DepositionFeb 6, 1987Processing site: BNL
Revision 1.0Apr 16, 1987Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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
Revision 1.4Oct 16, 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: ALPHA-CHYMOTRYPSIN A
B: ALPHA-CHYMOTRYPSIN A
C: ALPHA-CHYMOTRYPSIN A
E: ALPHA-CHYMOTRYPSIN A
F: ALPHA-CHYMOTRYPSIN A
G: ALPHA-CHYMOTRYPSIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8258
Polymers50,5256
Non-polymers3002
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16680 Å2
ΔGint-127 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.270, 67.160, 65.910
Angle α, β, γ (deg.)90.00, 101.68, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.91789, 0.00797, 0.39675), (0.01307, -0.9998, -0.010166), (0.39661, 0.014519, -0.917869)
Vector: -10.1, 40.3, 47.9)
Details6CHA THE TRANSFORMATION PROVIDED ON THE *MTRIX* RECORDS BELOW 6CHA YIELDS APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED 6CHA TO CHAIN *B*. 6CHA

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Components

#1: Protein/peptide ALPHA-CHYMOTRYPSIN A


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


Mass: 13934.556 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#3: Protein ALPHA-CHYMOTRYPSIN A


Mass: 10074.495 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#4: Chemical ChemComp-PBA / PHENYLETHANE BORONIC ACID


Mass: 149.983 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11BO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal grow
*PLUS
Method: other / Details: Blevins, R.A., (1985) J. Mol. Biol., 260, 4264.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. all: 26342 / Num. obs: 22428 / % possible obs: 59.5 % / Num. measured all: 37693 / Rmerge(I) obs: 0.18

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→5 Å / Rfactor obs: 0.2
Refinement stepCycle: LAST / Resolution: 1.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 22 185 3679
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.03
X-RAY DIFFRACTIONp_angle_d0.06
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
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_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
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

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