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- PDB-3shc: Human Thrombin In Complex With UBTHR101 -

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Basic information

Entry
Database: PDB / ID: 3shc
TitleHuman Thrombin In Complex With UBTHR101
Components
  • Hirudin variant-2
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Serine Protease / Kringle / Hydrolase / Blood Coagulation / Blood Clotting / Convertion of Fibrinogen to Fibrin / Cleavage on Pairs of Basic Residues / Thrombin Inhibitor / Glycosylation / Blood / HYDROLASE-HYDROLASE INHIBITOR complex
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 / Regulation of Complement cascade / acute-phase response / 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 / serine-type endopeptidase inhibitor 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 / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Hirudin / Proteinase inhibitor I14, hirudin / Thrombin inhibitor hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain ...Hirudin / Proteinase inhibitor I14, hirudin / Thrombin inhibitor hirudin / Hirudin/antistatin / 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
D-PHENYLALANYL-N-[(4-CHLOROPYRIDIN-2-YL)METHYL]-L-PROLINAMIDE / Chem-B01 / Prothrombin / Hirudin variant-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBiela, A. / Heine, A. / Klebe, G.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin
Authors: Biela, A. / Khayat, M. / Tan, H. / Kong, J. / Heine, A. / Hangauer, D. / Klebe, G.
History
DepositionJun 16, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 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 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 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
L: Thrombin light chain
H: Thrombin heavy chain
I: Hirudin variant-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1937
Polymers35,5393
Non-polymers6544
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-31 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.400, 71.400, 72.800
Angle α, β, γ (deg.)90.00, 100.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-75-

ARG

21H-1154-

HOH

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Components

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Protein/peptide , 2 types, 2 molecules LI

#1: Protein/peptide Thrombin light chain


Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#3: Protein/peptide Hirudin variant-2


Mass: 1662.683 Da / Num. of mol.: 1 / Fragment: residues in UNP 60-72 / Source method: obtained synthetically
Details: Synthetic Fragment of Hirudin From Hirudo Medicinalis
Source: (synth.) Hirudo medicinalis (medicinal leech) / References: UniProt: P09945

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Protein / Sugars , 2 types, 2 molecules H

#2: Protein Thrombin heavy chain


Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / 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, 226 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-B01 / D-phenylalanyl-N-[(4-chloropyridin-2-yl)methyl]-L-prolinamide


Type: peptide-like, Peptide-like / Class: Thrombin inhibitor / Mass: 386.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23ClN4O2
References: D-PHENYLALANYL-N-[(4-CHLOROPYRIDIN-2-YL)METHYL]-L-PROLINAMIDE
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 21, 2009 / Details: Collimating mirror
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 27888 / Num. obs: 27888 / % possible obs: 99.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 17.13 Å2 / Rsym value: 0.079 / Net I/σ(I): 13.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 1411 / Rsym value: 0.4 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H8D

1h8d


Resolution: 1.9→24.845 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.8878 / SU ML: 0.18 / Cross valid method: Free R / σ(F): 0 / Phase error: 18.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1973 1297 4.86 %Random
Rwork0.1586 ---
all0.1605 28000 --
obs0.1605 26703 95.32 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.24 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 92.91 Å2 / Biso mean: 25.8342 Å2 / Biso min: 5.11 Å2
Baniso -1Baniso -2Baniso -3
1-3.7858 Å20 Å2-3.9907 Å2
2---2.4367 Å20 Å2
3----1.3491 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 43 223 2595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012492
X-RAY DIFFRACTIONf_angle_d1.0623386
X-RAY DIFFRACTIONf_chiral_restr0.073354
X-RAY DIFFRACTIONf_plane_restr0.004431
X-RAY DIFFRACTIONf_dihedral_angle_d16.64971
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.97610.27111190.19872582270187
1.9761-2.0660.19961370.17052790292795
2.066-2.17480.191770.16072841301897
2.1748-2.3110.21031310.15412798292995
2.311-2.48930.21611390.16232821296095
2.4893-2.73950.21271570.17332812296996
2.7395-3.13530.22131560.17072880303697
3.1353-3.94750.17981390.14642951309099
3.9475-24.84750.16911420.14532931307397
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)
10.1242-0.0136-0.04920.21550.09730.07190.16760.07-0.1454-0.0791-0.08540.08180.15350.02670.0060.12070.0356-0.04310.1271-0.03950.10846.7389-1.201512.7849
20.1013-0.05630.05510.1416-0.01610.07090.27230.214-0.0769-0.3346-0.1385-0.12450.09970.1710.1886-0.06360.34460.01180.0185-0.0030.120819.4335-1.575112.0574
30.2029-0.1583-0.04170.13580.01460.04490.06550.03350.1036-0.0414-0.0416-0.1005-0.04020.01980.04030.09140.01340.00920.0818-0.00150.111610.24336.659121.5309
40.296-0.04760.10250.0211-0.05630.24920.00570.0248-0.2145-0.00820.0260.15070.19410.026-0.09860.16410.0108-0.02650.06780.00890.12267.0061-7.893826.6353
50.05410.0023-0.03380.01950.00560.1573-0.0679-0.0697-0.04080.06460.11730.09570.1044-0.01040.00880.14740.01170.00970.10290.05230.154613.24-1.61125.762
60.4848-0.03960.13780.0845-0.04120.410.0489-0.1674-0.22050.00850.01110.05820.2012-0.0184-0.01330.09570.02030.00650.06030.01070.115910.2724-2.020926.3121
70.0139-0-0.0190.05870.00570.02870.0481-0.02770.047-0.02710.0129-0.0822-0.0420.0388-0.0180.0904-0.05180.01220.13360.02440.313127.00299.379421.8337
80.0054-0.0065-0.01750.01390.02350.05080.03240.0556-0.005-0.019-0.0038-0.00970.003-0.02850.00960.52250.21510.05850.521-0.13650.117811.0489-1.7391-2.552
92.0421-0.1235-0.07460.0211-0.0090.0209-0.0145-0.00590.0759-0.0216-0.00160.0619-0.0437-0.02350.00410.12490.02260.01370.08930.0130.15379.780617.382619.7592
100.0799-00.00020.05150.00340.03550.0213-0.04650.0136-0.0228-0.01530.0197-0.0313-0.04190.00750.11080.0706-0.00630.1173-0.01390.1144-2.2779.71425.14
110.00520.01-0.00740.04970.00510.0266-0.008-0.0093-0.0120.03380.00650.0757-0.0042-0.05210.01060.09850.04470.05160.18980.01120.1397-1.37666.074732.4866
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain H and resid 16:37)H16 - 37
2X-RAY DIFFRACTION2(chain H and resid 38:107)H38 - 107
3X-RAY DIFFRACTION3(chain H and resid 108:144)H108 - 144
4X-RAY DIFFRACTION4(chain H and resid 145:171)H145 - 171
5X-RAY DIFFRACTION5(chain H and resid 172:186D)H172 - 186
6X-RAY DIFFRACTION6(chain H and resid 187:232)H187 - 232
7X-RAY DIFFRACTION7(chain H and resid 233:246)H233 - 246
8X-RAY DIFFRACTION8(chain I and resid 54:64)I54 - 64
9X-RAY DIFFRACTION9(chain L and resid 1C:3)L1
10X-RAY DIFFRACTION10(chain L and resid 4:14B)L4 - 14
11X-RAY DIFFRACTION11(chain L and resid 14C:14K)L14

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