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- PDB-3s7h: Structure of thrombin mutant Y225P in the E* form -

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Basic information

Entry
Database: PDB / ID: 3s7h
TitleStructure of thrombin mutant Y225P in the E* form
Components(Prothrombin) x 2
KeywordsHYDROLASE / serine protease
Function / homology
Function and homology information


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-activated receptor signaling pathway / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / Defective F8 cleavage by thrombin / ligand-gated ion channel signaling pathway ...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-activated receptor signaling pathway / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / Defective F8 cleavage by thrombin / ligand-gated ion channel signaling pathway / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / positive regulation of blood coagulation / negative regulation of fibrinolysis / regulation of cytosolic calcium ion concentration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / negative regulation of proteolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of cytokine production involved in inflammatory response / positive regulation of release of sequestered calcium ion into cytosol / Peptide ligand-binding receptors / Regulation of Complement cascade / acute-phase response / positive regulation of receptor signaling pathway via JAK-STAT / Cell surface interactions at the vascular wall / lipopolysaccharide binding / growth factor activity / positive regulation of insulin secretion / platelet activation / positive regulation of protein localization to nucleus / response to wounding / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / heparin binding / regulation of cell shape / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of protein phosphorylation / positive regulation of cell growth / : / G alpha (q) signalling events / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / 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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNiu, W. / Chen, Z. / Gandhi, P. / Vogt, A. / Pozzi, N. / Pele, L.A. / Zapata, F. / 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: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structural identification of the pathway of long-range communication in an allosteric enzyme.
Authors: Gandhi, P.S. / Chen, Z. / Mathews, F.S. / Di Cera, E.
History
DepositionMay 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Jul 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 1.4Sep 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
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prothrombin
B: Prothrombin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1155
Polymers33,7102
Non-polymers4053
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-9 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.620, 57.620, 119.914
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein/peptide Prothrombin / 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: 3995.430 Da / Num. of mol.: 1 / Fragment: Thrombin light chain / Mutation: Y225P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: HPC4-modified pNUT / Organ (production host): kidney / References: UniProt: P00734, thrombin
#2: Protein Prothrombin / 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: 29714.160 Da / Num. of mol.: 1 / Fragment: Thrombin heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: HPC4-modified pNUT / Organ (production host): kidney / References: UniProt: P00734, thrombin
#3: 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 295 K / pH: 8
Details: 0.1 M Tris and 8% PEG 8000 , pH 8.0, 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
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 8, 2010
RadiationMonochromator: MIRROR+NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 30093 / % possible obs: 97.8 % / Observed criterion σ(I): -0.7 / Redundancy: 6.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 20.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.4 / % possible all: 86.3

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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 3BEI

3bei


Resolution: 1.9→28.53 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.382 / SU ML: 0.083 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): -0.7 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1518 5 %RANDOM
Rwork0.175 ---
obs0.176 28549 97.8 %-
all-29179 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 26 191 2441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222365
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.9723203
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35323.148108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97415422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.971521
X-RAY DIFFRACTIONr_chiral_restr0.080.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211800
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3861.51413
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7622288
X-RAY DIFFRACTIONr_scbond_it1.3213952
X-RAY DIFFRACTIONr_scangle_it2.2574.5915
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 78 -
Rwork0.275 1921 -
obs--89.12 %
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)
16.2448-1.8976-1.439.2106-1.28475.8026-0.0498-0.1480.46140.45390.097-0.2612-0.56270.0318-0.04720.21740.01850.03240.0551-0.00820.1303-14.68325.3210.617
231.8938-1.211110.386113.76873.292922.81731.85060.5901-2.37920.4661-0.80290.98691.6506-1.0704-1.04780.33760.0736-0.08520.1887-0.04840.4426-20.56328.7313.264
35.8318-1.7893-1.396621.3795-3.24144.7491-0.2848-0.409-0.51260.77110.1387-0.14570.2717-0.19080.14620.1408-0.02210.07770.21020.04780.1939-23.81512.84812.561
42.6806-0.4894-0.653.48150.20632.3182-0.00280.2948-0.0481-0.37010.0331-0.0195-0.1342-0.1115-0.03030.1105-0.0283-0.00270.1110.01970.1219-8.79316.502-6.922
51.2238-1.4844-0.42955.70051.23191.28150.02870.2120.211-0.39990.137-0.0986-0.2798-0.0792-0.16570.228-0.0110.01870.16990.06450.1643-8.23821.112-11.714
62.0055-0.7906-0.52993.95820.54722.89290.0430.05150.0597-0.10860.1038-0.39070.00520.2758-0.14680.0484-0.0408-0.02110.1231-0.00170.1437-0.89115.091-2.585
712.07414.18850.24320.417-0.08446.57160.141-0.5410.74890.2553-0.06880.3366-0.3214-0.2885-0.07220.27780.07340.02120.20640.0360.2204-6.9028.80416.504
83.6733-1.08240.49176.9425-1.5173.2226-0.02650.1851-0.0092-0.57320.07070.29880.3709-0.2387-0.04420.1201-0.0638-0.00510.147-0.00590.144-18.4857.9781.791
93.6310.8910.37988.41582.62293.45510.01290.3228-0.67370.0316-0.03620.41230.6724-0.15840.02330.3039-0.0675-0.01630.1979-0.00940.2787-12.065-4.5861.185
107.48650.8522-1.557712.2703-9.171225.9739-0.10560.4379-1.2371-0.11651.17881.25742.1339-3.5682-1.07320.3769-0.3376-0.01360.8007-0.00070.6163-23.4213.516-2.792
112.4395-0.6175-0.91022.99832.26396.7222-0.0439-0.0497-0.02620.10490.06750.04690.04720.0739-0.02370.0589-0.01820.00820.0420.01760.0888-12.06212.0595.45
123.883317.7285-11.827780.7695-23.9388-4.6872-0.185-0.239-0.0677-3.9642-0.32173.35851.1831-0.79830.50670.8594-0.1676-0.31060.4545-0.16610.7179-19.241-0.276-8.896
136.14471.17470.48494.3645-0.99524.24220.0114-0.11850.01940.31210.0401-0.375-0.00090.4305-0.05150.09580.0129-0.01280.1084-0.03360.1172-0.7348.5924.5
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 8
2X-RAY DIFFRACTION2A9 - 12
3X-RAY DIFFRACTION3A13 - 14
4X-RAY DIFFRACTION4B16 - 59
5X-RAY DIFFRACTION5B60 - 84
6X-RAY DIFFRACTION6B85 - 123
7X-RAY DIFFRACTION7B124 - 129
8X-RAY DIFFRACTION8B130 - 167
9X-RAY DIFFRACTION9B168 - 185
10X-RAY DIFFRACTION10B186 - 192
11X-RAY DIFFRACTION11B193 - 217
12X-RAY DIFFRACTION12B219 - 223
13X-RAY DIFFRACTION13B224 - 244

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