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- PDB-1acb: CRYSTAL AND MOLECULAR STRUCTURE OF THE BOVINE ALPHA-CHYMOTRYPSIN-... -

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Basic information

Entry
Database: PDB / ID: 1acb
TitleCRYSTAL AND MOLECULAR STRUCTURE OF THE BOVINE ALPHA-CHYMOTRYPSIN-EGLIN C COMPLEX AT 2.0 ANGSTROMS RESOLUTION
Components
  • ALPHA-CHYMOTRYPSIN
  • Eglin C
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / response to wounding / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / 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 ...Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chymotrypsinogen A / Eglin C
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBolognesi, M. / Frigerio, F. / Coda, A. / Pugliese, L. / Lionetti, C. / Menegatti, E. / Amiconi, G. / Schnebli, H.P. / Ascenzi, P.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Crystal and molecular structure of the bovine alpha-chymotrypsin-eglin c complex at 2.0 A resolution.
Authors: Frigerio, F. / Coda, A. / Pugliese, L. / Lionetti, C. / Menegatti, E. / Amiconi, G. / Schnebli, H.P. / Ascenzi, P. / Bolognesi, M.
#1: Journal: J.Mol.Recog. / Year: 1990
Title: X-Ray Crystal Structure of the Bovine Alpha-Chymotrypsin(Slash)Eglin C Complex at 2.6 Angstroms Resolution
Authors: Bolognesi, M. / Pugliese, L. / Gatti, G. / Frigerio, F. / Coda, A. / Antolini, L. / Schnebli, H.P. / Menegatti, E. / Amiconi, G. / Ascenzi, P.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Preliminary Crystallographic Data on the Complex of Bovine Alpha-Chymotrypsin with the Recombinant Proteinase Inhibitor Eglin C from Hirudo Medicinalis
Authors: Pugliese, L. / Gatti, G. / Bolognesi, M. / Coda, A. / Menegatti, E. / Schnebli, H.P. / Ascenzi, P. / Amiconi, G.
History
DepositionNov 8, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 700SHEET THE SHEETS PRESENTED AS *CH1* AND *CH2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA- ...SHEET THE SHEETS PRESENTED AS *CH1* AND *CH2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA-BARRELS. THIS IS REPRESENTED BY SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: ALPHA-CHYMOTRYPSIN
I: Eglin C


Theoretical massNumber of molelcules
Total (without water)33,7862
Polymers33,7862
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-12 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.300, 59.400, 42.500
Angle α, β, γ (deg.)90.00, 99.10, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES WITH POOR ELECTRON DENSITY: SER E 77, GLU E 78, ARG E 145, ALA E 149, ASN E 150, ARG E 154, GLN E 239, LYS I 8, HIS I 28, TYR I 49, ASN I 50.

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Components

#1: Protein ALPHA-CHYMOTRYPSIN


Mass: 25686.037 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 Eglin C


Mass: 8100.011 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / References: UniProt: P01051
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Compound detailsEGLIN C IS BOUND NON-COVALENTLY TO THE ACTIVE SITE OF THE ENZYME.
Has protein modificationY
Sequence detailsRESIDUES THR I 1, GLU I 2, PHE I 3, GLY I 4, SER I 5, GLU I 6, AND LEU I 7 OF EGLIN C HAVE BEEN ...RESIDUES THR I 1, GLU I 2, PHE I 3, GLY I 4, SER I 5, GLU I 6, AND LEU I 7 OF EGLIN C HAVE BEEN PROTEOLYTICALLY CLEAVED BY THE ENZYME DURING CRYSTALLIZATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop / Details: referred to J.Mol.Biol. 208.511-513
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlalpha chymotrypsin1drop
27 mg/mleglin c1drop
30.05 Mphosphate1drop
45 %(w/v)PEG40001dropcan be replaced with PEG6000
510 %PEG40001reservoircan be replaced with PEG6000

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 11 Å / Num. obs: 16841 / Observed criterion σ(I): 5 / Num. measured all: 31318 / Rmerge(I) obs: 0.04

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2→11 Å / Rfactor obs: 0.167 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 0 142 2431
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.97
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.018
X-RAY DIFFRACTIONt_gen_planes0.019
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.086
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 11 Å / Num. reflection all: 16833 / σ(F): 0 / Rfactor all: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_plane_restr0.019

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