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- PDB-3u98: Human Thrombin In Complex With MI001 -

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Basic information

Entry
Database: PDB / ID: 3u98
TitleHuman Thrombin In Complex With MI001
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 / Hirudin / 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
(2S)-1-[(2R)-2-(BENZYLSULFONYLAMINO)-5-GUANIDINO-PENTANOYL]-N-[(4-CARBAMIMIDOYLPHENYL)METHYL]PYRROLIDINE-2-CARBOXAMIDE / Chem-BJA / PHOSPHATE ION / Prothrombin / Hirudin variant-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBiela, A. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Thrombin Inhibition
Authors: Biela, A. / Sielaff, F. / Heine, A. / Steinmetzer, T. / Klebe, G.
History
DepositionOct 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 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 1.5Oct 16, 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)36,4588
Polymers35,5393
Non-polymers9195
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-35 kcal/mol
Surface area12560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.300, 71.500, 72.200
Angle α, β, γ (deg.)90.00, 100.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-1078-

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 , 4 types, 348 molecules

#5: Chemical ChemComp-BJA / (2S)-1-[(2R)-2-(benzylsulfonylamino)-5-guanidino-pentanoyl]-N-[(4-carbamimidoylphenyl)methyl]pyrrolidine-2-carboxamide


Type: Peptide-like / Class: Thrombin inhibitor / Mass: 556.680 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H36N8O4S
References: (2S)-1-[(2R)-2-(BENZYLSULFONYLAMINO)-5-GUANIDINO-PENTANOYL]-N-[(4-CARBAMIMIDOYLPHENYL)METHYL]PYRROLIDINE-2-CARBOXAMIDE
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
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: Nov 4, 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: 1.45→50 Å / Num. all: 59463 / Num. obs: 59463 / % possible obs: 95.2 % / Redundancy: 3 % / Biso Wilson estimate: 12.71 Å2 / Rsym value: 0.059 / Net I/σ(I): 17.4
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 3072 / Rsym value: 0.453 / % possible all: 97.9

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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: 1.45→22.562 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.9033 / SU ML: 0.15 / Cross valid method: Free R / σ(F): 0 / Phase error: 16.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1868 2856 5.06 %Random
Rwork0.1635 ---
all0.1647 59312 --
obs0.1647 56456 90.71 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.051 Å2 / ksol: 0.394 e/Å3
Displacement parametersBiso max: 93.4 Å2 / Biso mean: 21.8276 Å2 / Biso min: 6.11 Å2
Baniso -1Baniso -2Baniso -3
1-2.0086 Å20 Å2-2.4899 Å2
2---1.5837 Å20 Å2
3----0.4249 Å2
Refinement stepCycle: LAST / Resolution: 1.45→22.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 60 344 2732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082504
X-RAY DIFFRACTIONf_angle_d1.1173401
X-RAY DIFFRACTIONf_chiral_restr0.077353
X-RAY DIFFRACTIONf_plane_restr0.005432
X-RAY DIFFRACTIONf_dihedral_angle_d17.176977
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.4750.2471210.22952509263084
1.475-1.50180.2671200.22162459257984
1.5018-1.53070.21911310.20662540267187
1.5307-1.56190.19771400.18092625276588
1.5619-1.59590.21371530.16812631278491
1.5959-1.6330.15611270.16272745287292
1.633-1.67380.16161260.15662741286792
1.6738-1.71910.18141600.15552721288193
1.7191-1.76960.17921630.15482662282593
1.7696-1.82670.16871320.14732767289993
1.8267-1.8920.17291630.15792726288993
1.892-1.96770.18221530.1552767292094
1.9677-2.05720.1941500.1522828297895
2.0572-2.16560.16381690.15762811298096
2.1656-2.30110.20541460.15782799294595
2.3011-2.47860.20231470.16362813296095
2.4786-2.72760.18731330.17142799293294
2.7276-3.12150.20821530.1652775292893
3.1215-3.92930.16571470.14592687283491
3.9293-22.5650.18491220.17792195231773
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)
10.1946-0.15080.0830.33480.10110.13550.22440.2133-0.2072-0.1988-0.17410.17610.1073-0.04620.02080.1220.05-0.03010.1387-0.03780.11437.1013-1.58512.6081
20.6451-0.16680.03630.19930.17350.23230.22940.4292-0.0076-0.3593-0.1537-0.07020.22510.141-0.02330.18930.0739-0.00240.1769-0.00590.110215.7111.495610.3865
30.52080.01550.00010.63750.19260.62830.15240.2451-0.0008-0.1401-0.1231-0.11360.04920.1260.0010.10950.07020.01170.17580.00580.088218.6439-0.398611.6836
40.66410.19930.22590.55670.21510.1771-0.1157-0.31280.18210.27640.12090.03040.05720.08860.0160.16380.0415-0.02620.1538-0.03780.109911.81296.878633.9204
50.5922-0.59210.1430.7313-0.41330.3780.0169-0.0187-0.21380.07610.03210.11810.0953-0.0131-0.03640.12580.0072-0.00510.0853-0.00110.1248.962-8.291626.7366
60.8055-0.71920.11120.7054-0.00080.68950.0329-0.06080.02390.0390.001-0.03460.01210.0445-0.01530.0770.01050.00960.0651-0.00560.08415.35251.705426.0157
70.0024-0.0061-0.00330.0440.01240.00860.08580.1927-0.008-0.16480.0073-0.0082-0.046-0.05940.13980.42590.24860.09880.5604-0.1165-0.002111.9095-1.6947-3.0115
80.6953-0.12890.19850.1222-0.19690.3254-0.01160.0220.17680.07150.0184-0.1362-0.18970.14160.01830.1687-0.0041-0.03370.12880.01080.18849.785316.900419.7339
90.1444-0.0210.04750.042-0.02070.0733-0.0271-0.05630.0458-0.1006-0.10540.0264-0.0707-0.0605-0.12430.06230.15430.04490.0646-0.03270.1009-0.973814.616117.5896
100.3753-0.0794-0.59770.787-0.02061.07410.0242-0.1693-0.0720.11210.09270.29820.0337-0.3138-0.01590.12410.03380.0330.15910.00640.1484-2.2275.91829.9045
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 38:50)H38 - 50
3X-RAY DIFFRACTION3(chain H and resid 51:122)H51 - 122
4X-RAY DIFFRACTION4(chain H and resid 123:136)H123 - 136
5X-RAY DIFFRACTION5(chain H and resid 137:199)H137 - 199
6X-RAY DIFFRACTION6(chain H and resid 200:246)H200 - 246
7X-RAY DIFFRACTION7(chain I and resid 55:65)I55 - 65
8X-RAY DIFFRACTION8(chain L and resid 1C:3)L1
9X-RAY DIFFRACTION9(chain L and resid 4:12)L4 - 12
10X-RAY DIFFRACTION10(chain L and resid 13:14K)L13 - 14

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