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- PDB-4cha: STRUCTURE OF ALPHA-*CHYMOTRYPSIN REFINED AT 1.68 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 4cha
TitleSTRUCTURE OF ALPHA-*CHYMOTRYPSIN REFINED AT 1.68 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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.68 Å
AuthorsTsukada, H. / Blow, D.M.
Citation
Journal: J.Mol.Biol. / Year: 1985
Title: Structure of alpha-chymotrypsin refined at 1.68 A resolution.
Authors: Tsukada, H. / Blow, D.M.
#1: Journal: Acc.Chem.Res. / Year: 1976
Title: Structure and Mechanism of Chymotrypsin
Authors: Blow, D.M.
#2: Journal: Ann.N.Y.Acad.Sci. / Year: 1974
Title: The Active Centers of Serine Proteinases
Authors: Hartley, B.S.
#3: Journal: J.Mol.Biol. / Year: 1973
Title: Comparison of the Crystal Structures of Chymotrypsinogen-A and Alpha-Chymotrypsin
Authors: Wright, H.T.
#4: Journal: J.Mol.Biol. / Year: 1972
Title: Structure of Crystalline Alpha-Chymotrypsin. V. The Atomic Structure of Tosyl-Alpha-Chymotrypsin at 2 Angstroms Resolution
Authors: Birktoft, J.J. / Blow, D.M.
#5: Journal: J.Mol.Biol. / Year: 1972
Title: Structure of Crystalline Methyl-Chymotrypsin
Authors: Wright, C.S. / Hess, G.P. / Blow, D.M.
#6: 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.
#7: Journal: The Enzymes,Third Edition / Year: 1971
Title: Chymotrypsin-Chemical Properties and Catalysis
Authors: Hess, G.P.
#8: Journal: The Enzymes,Third Edition / Year: 1971
Title: The Structure of Chymotrypsin
Authors: Blow, D.M.
#9: 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.
#10: 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.
#11: Journal: Biochem.J. / Year: 1969
Title: The Study of Alpha-Chymotrypsin by X-Ray Diffraction
Authors: Blow, D.M.
#12: 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.
#13: 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.
#14: Journal: Nature / Year: 1967
Title: Three-Dimensional Structure of Tosyl-Alpha-Chymotrypsin
Authors: Matthews, B.W. / Sigler, P.B. / Henderson, R. / Blow, D.M.
History
DepositionNov 26, 1984Processing site: BNL
Revision 1.0Apr 1, 1985Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 23, 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


Theoretical massNumber of molelcules
Total (without water)50,5256
Polymers50,5256
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16600 Å2
ΔGint-124 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.230, 67.390, 65.990
Angle α, β, γ (deg.)90.00, 101.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (0.9158, 0.40163), (-1), (0.40163, -0.9158) / Vector: -12.86, 61.36)
Details4CHA THE TWO INDEPENDENT MOLECULES IN THE ASYMMETRIC UNIT HAVE 4CHA BEEN ASSIGNED CHAIN IDENTIFIERS *A* AND *B*. THE 4CHA TRANSFORMATION SUPPLIED IN THE *MTRIX* RECORDS BELOW WILL 4CHA GENERATE APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED 4CHA TO CHAIN *A*. 4CHA

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Compound details4CHA THE ALPHA CHYMOTRYPSIN MOLECULE IS COMPRISED OF THREE 4CHA POLYPEPTIDE CHAINS WHICH ARE ...4CHA THE ALPHA CHYMOTRYPSIN MOLECULE IS COMPRISED OF THREE 4CHA POLYPEPTIDE CHAINS WHICH ARE DERIVED FROM THE ZYMOGEN OF 4CHA THIS ENZYME BY EXCISION OF RESIDUES 14-15 AND 147-148. TO 4CHA ASSIGN SEPARATE CHAIN IDENTIFIERS TO THE THREE CHAINS 4CHA WOULD OBSCURE THIS RELATIONSHIP AND SO THIS WAS NOT DONE. 4CHA CHAIN TERMINATOR RECORDS WERE INSERTED AFTER RESIDUES 146 4CHA AND 245 TO INDICATE EXPLICIT TERMINI AND THE SPECIAL CODE 4CHA EXC WAS USED IN THE SEQRES RECORDS TO DENOTE THE EXCISIONS. 4CHA
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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 4.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 Mcitrate11
248 %satammonium sulfate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.68 Å / Lowest resolution: 8 Å / Num. obs: 32162 / Observed criterion σ(I): 3 / Num. measured all: 44408 / Rmerge(I) obs: 0.087

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Processing

RefinementHighest resolution: 1.68 Å
Refinement stepCycle: LAST / Highest resolution: 1.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 0 85 3591
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 35274 / σ(I): 3 / Rfactor obs: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d0.04

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