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- PDB-3qgn: The allosteric E*-E equilibrium is a key property of the trypsin fold -

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Basic information

Entry
Database: PDB / ID: 3qgn
TitleThe allosteric E*-E equilibrium is a key property of the trypsin fold
Components
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsHYDROLASE / Serine protease
Function / homology
Function and homology information


positive regulation of lipid kinase activity / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / positive regulation of cell population proliferation / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. ...Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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
IODIDE ION / Prothrombin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNiu, W. / Gohara, D. / Chen, Z. / Di Cera, E.
Citation
Journal: Biochemistry / Year: 2011
Title: Crystallographic and kinetic evidence of allostery in a trypsin-like protease.
Authors: Niu, W. / Chen, Z. / Gandhi, P.S. / Vogt, A.D. / Pozzi, N. / Pelc, L.A. / Zapata, F. / Di Cera, E.
#1: Journal: J.Biol.Chem. / Year: 2009
Title: Mutant N143P reveals how Na+ activates thrombin.
Authors: Niu, W. / Chen, Z. / Bush-Pelc, L.A. / Bah, A. / Gandhi, P.S. / Di Cera, E.
History
DepositionJan 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thrombin light chain
B: Thrombin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,42810
Polymers33,4102
Non-polymers1,0188
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-18 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.179, 47.980, 52.011
Angle α, β, γ (deg.)90.00, 94.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein/peptide / Protein / Sugars , 3 types, 3 molecules AB

#1: Protein/peptide Thrombin light chain / Coagulation factor II / Activation peptide fragment 1 / Activation peptide fragment 2 / Thrombin ...Coagulation factor II / Activation peptide fragment 1 / Activation peptide fragment 2 / Thrombin light chain / Thrombin heavy chain


Mass: 3647.075 Da / Num. of mol.: 1 / Fragment: unp residues 333-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell line (production host): BHK CELLS / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P00734, thrombin
#2: Protein Thrombin heavy chain / Coagulation factor II / Activation peptide fragment 1 / Activation peptide fragment 2 / Thrombin ...Coagulation factor II / Activation peptide fragment 1 / Activation peptide fragment 2 / Thrombin light chain / Thrombin heavy chain


Mass: 29763.234 Da / Num. of mol.: 1 / Fragment: unp residues 364-622 / Mutation: N143P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell line (production host): BHK CELLS / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P00734, thrombin
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 157 molecules

#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.2 M NH4I and 20 % PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 13, 2011
RadiationMonochromator: Mirror (Varimax HF) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 17851 / Num. obs: 17583 / % possible obs: 98.5 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 4.3 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.1-2.143.40.166.6849197.3
2.14-2.183.50.1617.2875198.1
2.18-2.223.60.1527.8856197.3
2.22-2.263.70.1438.4884197.9
2.26-2.313.80.1398.9850198
2.31-2.373.80.1249.9883197.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPfrom ccp4phasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3JZ1

3jz1


Resolution: 2.1→31 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.43 / SU ML: 0.144 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): -0.5 / σ(I): -0.5 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 892 5.1 %RANDOM
Rwork0.1888 ---
obs0.1914 16480 97.86 %-
all-16842 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.499 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.25 Å2
2---0.19 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 21 150 2410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222313
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.973125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1835273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00423.211109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.77415410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2391520
X-RAY DIFFRACTIONr_chiral_restr0.0910.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211754
X-RAY DIFFRACTIONr_mcbond_it0.5811.51373
X-RAY DIFFRACTIONr_mcangle_it1.11722215
X-RAY DIFFRACTIONr_scbond_it1.8913940
X-RAY DIFFRACTIONr_scangle_it3.0344.5910
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 74 -
Rwork0.204 1175 -
obs-1249 96.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
111.26031.18271.486114.8923-3.61682.49720.017-1.0393-0.72240.64720.2080.45120.5524-0.0197-0.22510.35490.0640.03540.21490.05540.1027-10.449-34.42821.496
210.2163-3.67054.153910.02943.57612.7578-0.02280.1676-0.1827-0.1027-0.1106-0.47370.29250.68040.13340.08510.03990.02670.1911-0.02230.0958-0.705-33.46116.767
38.5442-5.5372-2.714127.65049.837410.7377-0.0798-0.05590.45360.52520.3583-1.5471-0.18960.6399-0.27850.1105-0.06330.01560.28640.04190.1678-1.125-18.0617.252
44.42980.06850.05772.86960.21122.11270.07220.42790.0668-0.46770.03270.27460.1132-0.0476-0.10490.1832-0.02740.01520.170.00740.0796-21.953-28.3957.619
57.8666-4.68211.20577.30351.13493.26150.22360.5706-0.8065-1.0224-0.21391.0353-0.16640.0361-0.00970.3157-0.0717-0.10520.28330.03080.2023-30.696-30.8214.886
65.441311.9804-5.846129.3136-2.879521.4012-0.72960.9470.0633-2.68851.56860.29511.08070.3075-0.8390.73520.0581-0.07720.6447-0.11970.3785-13.855-38.7970.157
72.897-0.25050.81343.30920.32971.6160.0241-0.1586-0.1527-0.04140.08410.4180.0666-0.1816-0.10820.1176-0.03510.0550.18250.04330.1059-25.587-27.90816.702
83.3862-0.86310.54616.51390.28791.5971-0.06940.19050.2039-0.4071-0.04850.3647-0.18260.14480.11790.1787-0.03350.03940.15920.04480.0941-14.851-13.86610.806
915.64780.8217-5.88094.073-1.36278.73190.0078-0.04241.0604-0.2561-0.01420.1448-0.49340.18570.00650.2288-0.00050.03240.12890.03030.2676-18.291-9.18714.654
108.1908-1.3134.69251.9629-0.97475.055-0.06710.13310.1811-0.05630.0413-0.0356-0.11560.0730.02580.0854-0.01870.06570.1152-0.00430.0518-14.679-21.06716.689
116.14823.9826-1.53759.3361-4.6195.6961-0.1073-0.15160.2017-0.19370.03210.0473-0.0326-0.07640.07520.07430.01940.06740.1279-0.01360.0875-22.707-17.35116.985
121.75527.906714.880320.60844.758468.43850.5617-0.1822-0.41711.72580.6486-1.05113.7974-0.5732-1.21030.7719-0.58240.43261.16660.02040.7821-32.899-36.36425.744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION2A6 - 12
3X-RAY DIFFRACTION3A13 - 14
4X-RAY DIFFRACTION4B16 - 59
5X-RAY DIFFRACTION5B60 - 70
6X-RAY DIFFRACTION6B71 - 80
7X-RAY DIFFRACTION7B81 - 129
8X-RAY DIFFRACTION8B130 - 175
9X-RAY DIFFRACTION9B176 - 193
10X-RAY DIFFRACTION10B194 - 217
11X-RAY DIFFRACTION11B219 - 242
12X-RAY DIFFRACTION12B243 - 247

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