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- PDB-1ggd: CRYSTAL STRUCTURE OF GAMMA CHYMOTRYPSIN WITH N-ACETYL-LEUCIL-PHEN... -

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Basic information

Entry
Database: PDB / ID: 1ggd
TitleCRYSTAL STRUCTURE OF GAMMA CHYMOTRYPSIN WITH N-ACETYL-LEUCIL-PHENYLALANINE ALDEHYDE BOUND AT THE ACTIVE SITE
Components(GAMMA CHYMOTRYPSIN) x 3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CHYMOTRYPSIN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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-FAF / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsNeidhart, D. / Wei, Y. / Cassidy, C. / Lin, J. / Cleland, W.W. / Frey, P.A.
CitationJournal: Biochemistry / Year: 2000
Title: Correlation of low-barrier hydrogen bonding and oxyanion binding in transition state analogue complexes of chymotrypsin.
Authors: Neidhart, D. / Wei, Y. / Cassidy, C. / Lin, J. / Cleland, W.W. / Frey, P.A.
History
DepositionAug 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Jun 27, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.7Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)25,4065
Polymers25,0053
Non-polymers4002
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-78 kcal/mol
Surface area10000 Å2
MethodPISA
2
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)50,81110
Polymers50,0116
Non-polymers8014
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area17850 Å2
ΔGint-173 kcal/mol
Surface area17790 Å2
MethodPISA
3
A: GAMMA CHYMOTRYPSIN

A: GAMMA CHYMOTRYPSIN

B: GAMMA CHYMOTRYPSIN
C: GAMMA CHYMOTRYPSIN
hetero molecules

B: GAMMA CHYMOTRYPSIN
C: GAMMA CHYMOTRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,81110
Polymers50,0116
Non-polymers8014
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation5_545-x+1/2,y-1/2,-z+1/21
crystal symmetry operation6_555x+1/2,-y+1/2,-z+1/21
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area16320 Å2
ΔGint-160 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.600, 69.600, 97.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-582-

HOH

21B-658-

HOH

31C-652-

HOH

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide GAMMA CHYMOTRYPSIN


Mass: 996.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin

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Protein , 2 types, 2 molecules BC

#2: Protein GAMMA CHYMOTRYPSIN


Mass: 13934.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin
#3: Protein GAMMA CHYMOTRYPSIN


Mass: 10074.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin

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Non-polymers , 3 types, 217 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FAF / 2-ACETYLAMINO-4-METHYL-PENTANOIC ACID (1-FORMYL-2-PHENYL-ETHYL)-AMIDE


Mass: 304.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H24N2O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: ammonium sulfate, potassium phosphate, pH 7.0, vapor diffusion, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
175 %satammonium sulfate1reservoir
210 mMpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 29, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 38043 / Num. obs: 34112 / % possible obs: 88 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.043
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.184 / % possible all: 55.1
Reflection
*PLUS
Num. obs: 38043
Reflection shell
*PLUS
% possible obs: 55.1 %

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Processing

Software
NameVersionClassification
FRAMBOdata collection
XDSdata reduction
XCALIBREmodel building
X-PLOR3.5refinement
XDSdata scaling
XCALIBREphasing
RefinementResolution: 1.5→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Initial coordinates for this structure were derived from the model of G. Cohen et al. (PDB entry 2GCH). Secondary structure elements and sequence data are identical to those of entry 2GCH. ...Details: Initial coordinates for this structure were derived from the model of G. Cohen et al. (PDB entry 2GCH). Secondary structure elements and sequence data are identical to those of entry 2GCH. RESIDUES ALA 149 and ASN 150 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.212 3419 -
Rwork0.182 --
all-38043 -
obs-34112 88 %
Refinement stepCycle: LAST / Resolution: 1.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 27 215 1980
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.3
Software
*PLUS
Name: X-PLOR / Version: 3.5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.3

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