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- PDB-1dlk: CRYSTAL STRUCTURE ANALYSIS OF DELTA-CHYMOTRYPSIN BOUND TO A PEPTI... -

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Basic information

Entry
Database: PDB / ID: 1dlk
TitleCRYSTAL STRUCTURE ANALYSIS OF DELTA-CHYMOTRYPSIN BOUND TO A PEPTIDYL CHLOROMETHYL KETONE INHIBITOR
Components
  • Thrombin heavy chain
  • Thrombin light chain
  • peptidic inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Delta-chymotrypsin / peptidic inhibior / chloromethyl ketone / HYDROLASE / 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
Z-GLY-GLY-PHE-CHLOROMETHYL KETONE (BOUND FORM) / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.14 Å
AuthorsMac Sweeney, A. / Birrane, G. / Walsh, M.A. / O'Connell, T. / Malthouse, J.P.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystal structure of delta-chymotrypsin bound to a peptidyl chloromethyl ketone inhibitor.
Authors: Mac Sweeney, A. / Birrane, G. / Walsh, M.A. / O'Connell, T. / Malthouse, J.P. / Higgins, T.M.
History
DepositionDec 10, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Sep 12, 2018Group: Advisory / Data collection / Structure summary
Category: diffrn_source / pdbx_molecule_features ...diffrn_source / pdbx_molecule_features / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thrombin light chain
B: Thrombin heavy chain
C: Thrombin light chain
D: Thrombin heavy chain
E: peptidic inhibitor
F: peptidic inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8887
Polymers51,8526
Non-polymers351
Water5,062281
1
A: Thrombin light chain
B: Thrombin heavy chain
E: peptidic inhibitor
hetero molecules

C: Thrombin light chain
D: Thrombin heavy chain
F: peptidic inhibitor


Theoretical massNumber of molelcules
Total (without water)51,8887
Polymers51,8526
Non-polymers351
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z+1/41
Buried area6920 Å2
ΔGint-41 kcal/mol
Surface area18210 Å2
MethodPISA
2
A: Thrombin light chain
B: Thrombin heavy chain
E: peptidic inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9624
Polymers25,9263
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-12 kcal/mol
Surface area10320 Å2
MethodPISA
3
C: Thrombin light chain
D: Thrombin heavy chain
F: peptidic inhibitor


Theoretical massNumber of molelcules
Total (without water)25,9263
Polymers25,9263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-12 kcal/mol
Surface area10180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.170, 121.170, 116.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.03684, -0.49183, 0.86991), (0.99791, -0.02806, -0.05812), (0.05299, 0.87024, 0.48977)
Vector: 0.5685, -0.14946, -0.35459)

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Components

#1: Protein/peptide Thrombin light chain


Mass: 1253.511 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-13 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin
#2: Protein Thrombin heavy chain


Mass: 24206.271 Da / Num. of mol.: 2 / Fragment: RESIDUES 16-245 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin
#3: Protein/peptide peptidic inhibitor


Type: Peptide-like / Class: Enzyme inhibitor / Mass: 466.359 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: this sequence was synthetically constructed / References: Z-GLY-GLY-PHE-CHLOROMETHYL KETONE (BOUND FORM)
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PEPTIDIC INHIBITOR BINDS TO THROMBIN THROUGH TWO COVALENT BONDS: A BOND BETWEEN 0QE AND HIS 57 ...THE PEPTIDIC INHIBITOR BINDS TO THROMBIN THROUGH TWO COVALENT BONDS: A BOND BETWEEN 0QE AND HIS 57 AND A HEMIKETAL BETWEEN HPH AND SER 195.
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: 4.18 Å3/Da / Density % sol: 70.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.6 M ammonium sulfate, 200 mM MES-HCl, 10 mM CoCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
22.6 Mammonium sulfate1reservoir
310 mM1reservoirCoCl2
4200 mMMES-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.911
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.911 Å / Relative weight: 1
ReflectionResolution: 2.14→40 Å / Num. all: 48065 / Num. obs: 39978 / % possible obs: 82.7 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 22.6
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 5 % / Rmerge(I) obs: 0.43 / Num. unique all: 2370 / % possible all: 100
Reflection
*PLUS
Num. obs: 48065 / % possible obs: 99.6 % / Num. measured all: 308959
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 4.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementResolution: 2.14→19.9 Å / σ(F): 0 / Stereochemistry target values: John Priestle / Details: Used maximum likelihood procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2428 -RANDOM
Rwork0.207 ---
all0.207 60282 --
obs0.206 45515 75.5 %-
Refinement stepCycle: LAST / Resolution: 2.14→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3624 0 1 281 3906
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d2
X-RAY DIFFRACTIONp_bond_d0.018
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / Num. reflection obs: 48013 / σ(F): 0 / Num. reflection Rfree: 2370 / % reflection Rfree: 10 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.251
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 2

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