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- PDB-3s7k: Structure of thrombin mutant Y225P in the E form -

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Basic information

Entry
Database: PDB / ID: 3s7k
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 / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin ...cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / ligand-gated ion channel signaling pathway / 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 / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of proteolysis / negative regulation of cytokine production involved in inflammatory response / Peptide ligand-binding receptors / Regulation of Complement cascade / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Cell surface interactions at the vascular wall / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / lipopolysaccharide binding / 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 / regulation of cell shape / heparin binding / : / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of cell growth / blood microparticle / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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: J.Biol.Chem. / Year: 2004
Title: Molecular dissection of Na+ binding to thrombin.
Authors: Pineda, A.O. / Carrell, C.J. / Bush, L.A. / Prasad, S. / Caccia, S. / Chen, Z.W. / 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 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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
C: Prothrombin
D: Prothrombin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7428
Polymers67,4194
Non-polymers3224
Water6,918384
1
A: Prothrombin
B: Prothrombin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8714
Polymers33,7102
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-8 kcal/mol
Surface area13700 Å2
MethodPISA
2
C: Prothrombin
D: Prothrombin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8714
Polymers33,7102
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-8 kcal/mol
Surface area13620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.937, 86.813, 100.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-402-

K

21C-402-

K

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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.: 2 / Fragment: Thrombin light chain / Mutation: Y225P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / 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.: 2 / Fragment: Thrombin heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P00734, thrombin
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.2 M K Formate, 20 % PEG 3350, pH 7.3, 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: Feb 17, 2011
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. all: 43725 / Num. obs: 43419 / % possible obs: 99.3 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 6.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 27.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-1.934.70.3054198.2
1.93-1.974.80.2734.7198.4
1.97-2.015.10.2335.7198.7
2.01-2.055.20.2186.4199
2.05-2.095.50.1927.8199.1
2.09-2.145.70.1768.9199.4

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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 1SHH

1shh


Resolution: 1.9→35.67 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.089 / SU ML: 0.096 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -0.5 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2179 5 %RANDOM
Rwork0.175 ---
obs0.177 41076 99 %-
all-41512 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.17 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4582 0 18 384 4984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224713
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9646362
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9325561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27723.229223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28215842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9671542
X-RAY DIFFRACTIONr_chiral_restr0.0880.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213572
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_it0.6381.52823
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16924549
X-RAY DIFFRACTIONr_scbond_it1.74431890
X-RAY DIFFRACTIONr_scangle_it2.7934.51813
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
Rfree0.23 130 -
Rwork0.192 2923 -
obs--96.46 %
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)
15.23910.817-1.53225.85033.25639.4486-0.13070.61320.1106-0.4458-0.05250.3272-0.3295-0.50370.18320.179-0.0489-0.00440.2364-0.00480.15248.22710.7250.734
22.80681.6143-2.09213.8912-1.5096.9345-0.25150.455-0.4259-0.73930.1852-0.26020.42-0.00770.06630.2594-0.04030.03910.2143-0.09870.24978.624-0.2958.346
32.09570.75860.36641.80381.62323.5308-0.07710.1805-0.0527-0.16360.2273-0.2805-0.23820.4393-0.15020.1607-0.06410.03550.1885-0.00710.20522.83118.95210.282
46.02556.43630.898419.5876.83765.27150.5499-0.4516-0.24791.4957-0.2553-1.1891-0.02130.6666-0.29460.4158-0.1887-0.04030.33230.03720.234826.82421.3634.619
51.7311.02470.28272.00840.45571.601-0.09150.11160.1065-0.25720.0934-0.0623-0.27550.1924-0.00190.1816-0.02580.02170.15480.00440.192118.19918.73911.588
62.65540.868-1.8463.22590.21346.6870.2075-0.3842-0.17620.4585-0.1723-0.20150.18420.2358-0.03520.1285-0.0383-0.02990.16680.04560.213415.5767.17723.31
74.40251.04541.31224.17811.31144.34830.1867-0.6176-0.03840.6109-0.1596-0.14610.16480.1647-0.0270.2105-0.0896-0.01610.27450.02360.18514.91713.2129.81
814.34574.7656-2.106913.3358-5.673414.86840.1293-1.6206-2.17060.5998-0.1253-1.43561.66660.922-0.00390.50520.129-0.11730.40840.19670.691122.7272.72423.586
96.40282.91042.09213.22561.36532.5096-0.02920.0374-0.09530.00730.0287-0.0723-0.06070.01850.00050.0802-0.01980.00880.07150.0020.100311.50711.84914.361
104.4760.1689-0.54857.9227-1.56094.9571-0.1306-0.8768-0.78840.9635-0.4357-1.73120.7461.05430.56620.42830.0811-0.15450.47630.22480.630112.2820.45219.414
1110.0644-6.77243.80811.2223-1.91596.339-0.94790.1370.2816-0.22020.44920.6236-0.8023-0.4940.49870.3873-0.1161-0.18290.36440.04060.34725.48117.12752.718
122.31331.3261-1.61343.5241-4.15199.0274-0.32350.6835-0.2517-0.80120.1912-0.06570.6651-0.14310.13230.3555-0.11690.03480.3574-0.10090.238.6251.86556.559
132.07620.31050.05422.5774-0.01541.8337-0.28980.2479-0.3396-0.12160.1575-0.38320.01620.58650.13230.2332-0.09590.04970.3604-0.00480.284422.0412.43657.905
142.33131.02251.46510.96751.6583.6452-0.35680.35370.3436-0.31670.2634-0.0363-0.4960.3130.09350.326-0.1145-0.04890.23370.04640.320723.11325.65464.752
154.85523.2132.098221.324810.05746.7146-0.03350.34420.01540.10270.0942-1.2405-0.26470.5087-0.06070.3422-0.2209-0.03570.31820.10230.281925.75623.04355.615
162.64391.15590.03862.35880.94125.7227-0.28190.42240.3942-0.42210.25040.0626-0.50150.43850.03160.3082-0.1372-0.03720.23910.08680.276620.95425.79859.789
172.23071.12480.28732.17770.27521.0767-0.19280.18820.2784-0.15470.07190.1698-0.2384-0.02070.12090.1696-0.0211-0.02520.14780.01890.207611.15518.17863.727
189.5003-2.75212.436713.23297.47226.3804-0.50170.44790.52310.27791.6181-2.6043-0.12151.7808-1.11650.2005-0.1821-0.00171.08230.05591.000931.40810.17863.395
192.92410.9935-0.04753.13281.45817.28140.0805-0.3261-0.12670.4915-0.0838-0.14360.15130.07340.00320.1932-0.03510.00920.16150.02280.201213.9146.20676.982
202.99580.66080.7172.4756-0.36842.24770.0049-0.2159-0.22550.3105-0.0317-0.25010.30850.180.02680.2107-0.0145-0.02090.22360.02040.23517.2897.39577.831
213.66041.95910.68653.81610.29083.264-0.1588-0.0073-0.11230.11580.0388-0.2248-0.04030.21360.11990.107-0.01620.00530.1104-0.00040.127414.95911.39868.583
2210.25564.0047-2.702612.4665-4.23997.32750.16810.46171.5935-0.2319-0.06781.2229-0.6786-0.4788-0.10040.29770.0736-0.11920.1743-0.00810.54145.57727.77266.97
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 14
3X-RAY DIFFRACTION3B16 - 60
4X-RAY DIFFRACTION4B61 - 73
5X-RAY DIFFRACTION5B74 - 153
6X-RAY DIFFRACTION6B154 - 170
7X-RAY DIFFRACTION7B171 - 185
8X-RAY DIFFRACTION8B186 - 193
9X-RAY DIFFRACTION9B194 - 217
10X-RAY DIFFRACTION10B219 - 246
11X-RAY DIFFRACTION11C1 - 4
12X-RAY DIFFRACTION12C5 - 14
13X-RAY DIFFRACTION13D16 - 35
14X-RAY DIFFRACTION14D36 - 60
15X-RAY DIFFRACTION15D61 - 73
16X-RAY DIFFRACTION16D74 - 96
17X-RAY DIFFRACTION17D97 - 139
18X-RAY DIFFRACTION18D140 - 156
19X-RAY DIFFRACTION19D157 - 171
20X-RAY DIFFRACTION20D172 - 190
21X-RAY DIFFRACTION21D191 - 230
22X-RAY DIFFRACTION22D231 - 246

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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