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- PDB-2cha: THE STRUCTURE OF CRYSTALLINE ALPHA-CHYMOTRYPSIN, $V.THE ATOMIC ST... -

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Entry
Database: PDB / ID: 2cha
TitleTHE STRUCTURE OF CRYSTALLINE ALPHA-CHYMOTRYPSIN, $V.THE ATOMIC STRUCTURE OF TOSYL-ALPHA-CHYMOTRYPSIN AT 2 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 / 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
PARA-TOLUENE SULFONATE / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBirktoft, J.J. / Blow, D.M.
Citation
Journal: J.Mol.Biol. / Year: 1972
Title: Structure of crystalline -chymotrypsin. V. The atomic structure of tosyl- -chymotrypsin at 2 A resolution.
Authors: Birktoft, J.J. / Blow, D.M.
#1: Journal: Nature / Year: 1967
Title: Three-Dimensional Structure of Tosyl-Alpha-Chymotrypsin
Authors: Matthews, B.W. / Sigler, P.B. / Henderson, R. / Blow, D.M.
#2: Journal: J.Mol.Biol. / Year: 1968
Title: Structure of Crystalline Alpha-Chymotrypsin, II.A Preliminary Report Including a Hypothesis for the Activation Mechanism
Authors: Sigler, P.B. / Blow, D.M. / Matthews, B.W. / Henderson, R.
#3: Journal: J.Mol.Biol. / Year: 1969
Title: Structure of Crystalline Alpha-Chymotrypsin, III.Crystallographic Studies of Substrates and Inhibitors Bound to the Active Site of Alpha-Chymotrypsin
Authors: Steitz, T.A. / Henderson, R. / Blow, D.M.
#4: Journal: J.Mol.Biol. / Year: 1970
Title: Structure of Crystalline Alpha-Chymotrypsin, Iv.The Structure of Indoleacryloyl-Alpha-Chymotrypsin and its Relevance to the Hydrolytic Mechanism of the Enzyme
Authors: Henderson, R.
#5: Journal: Acc.Chem.Res. / Year: 1976
Title: Structure and Mechanism of Chymotrypsin
Authors: Blow, D.M.
#6: Journal: Ann.N.Y.Acad.Sci. / Year: 1974
Title: The Active Centers of Serine Proteinases
Authors: Hartley, B.S.
#7: Journal: J.Mol.Biol. / Year: 1973
Title: Comparison of the Crystal Structures of Chymotrypsinogen-A and Alpha-Chymotrypsin
Authors: Wright, H.T.
#8: Journal: J.Mol.Biol. / Year: 1972
Title: Structure of Crystalline Methyl-Chymotrypsin
Authors: Wright, C.S. / Hess, G.P. / Blow, D.M.
#9: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: Alpha-Chymotrypsin,What Can We Learn About Catalysis from X-Ray Diffraction (Query).
Authors: Henderson, R. / Wright, C.S. / Hess, G.P. / Blow, D.M.
#10: Journal: The Enzymes,Third Edition / Year: 1971
Title: The Structure of Chymotrypsin
Authors: Blow, D.M.
#11: Journal: The Enzymes,Third Edition / Year: 1971
Title: Chymotrypsin-Chemical Properties and Catalysis
Authors: Hess, G.P.
#12: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1970
Title: The Structure of Alpha-Chymotrypsin
Authors: Birktoft, J.J. / Blow, D.M. / Henderson, R. / Steitz, T.A.
#13: Journal: Biochem.J. / Year: 1969
Title: The Study of Alpha-Chymotrypsin by X-Ray Diffraction
Authors: Blow, D.M.
#14: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
#15: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionJan 1, 1975Processing site: BNL
Revision 1.0Jan 18, 1977Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 24, 2011Group: Non-polymer description
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_database_status / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_database_status.process_site / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_planes.rmsd / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][3] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ncs_oper.vector[3] / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Nov 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

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)50,8708
Polymers50,5256
Non-polymers3442
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17050 Å2
ΔGint-123 kcal/mol
Surface area18350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.100, 67.400, 65.900
Angle α, β, γ (deg.)90.00, 101.70, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: THE SIDE-CHAIN HYDROXYL GROUP OF SERINE 195 IS TOSYLATED IN THIS STRUCTURE. COORDINATES FOR THE P-TOLUENE-SULFONATE GROUP ARE GIVEN BELOW IN THE *HETATM* RECORDS FOR THE GROUP *TOS*.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (0.917752, 0.397154), (-1), (0.397154, -0.917752) / Vector: -9.99729, 40.38, 48.27433)

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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 (domestic 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 (domestic 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 (domestic cattle) / References: UniProt: P00766, chymotrypsin
#4: Chemical ChemComp-TSU / PARA-TOLUENE SULFONATE


Mass: 172.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Compound details2CHA THE ALPHA CHYMOTRYPSIN MOLECULE IS COMPRISED OF THREE 2CHA POLYPEPTIDE CHAINS WHICH ARE ...2CHA THE ALPHA CHYMOTRYPSIN MOLECULE IS COMPRISED OF THREE 2CHA POLYPEPTIDE CHAINS WHICH ARE DERIVED FROM THE ZYMOGEN OF 2CHA THIS ENZYME BY EXCISION OF RESIDUES 14-15 AND 147-148. TO 2CHA ASSIGN SEPARATE CHAIN IDENTIFIERS TO THE THREE CHAINS 2CHA WOULD OBSCURE THIS RELATIONSHIP AND SO THIS WAS NOT DONE. 2CHA CHAIN TERMINATOR RECORDS WERE INSERTED AFTER RESIDUES 146 2CHA AND 245 TO INDICATE EXPLICIT TERMINI AND THE SPECIAL CODE 2CHA EXC WAS USED IN THE SEQRES RECORDS TO DENOTE THE EXCISIONS. 2CHA RESIDUES 9 THROUGH 13 ARE NOT VISIBLE IN THE ELECTRON 2CHA DENSITY MAP AND SO ARE OMITTED, CONSEQUENTLY THE TER RECORD 2CHA WHICH WOULD HAVE APPEARED AFTER RESIDUE 13 IS ALSO OMITTED. 2CHA
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: 4.23 Å3/Da / Density % sol: 70.89 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 20 50 3542

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