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- PDB-3rly: Human Thrombin in complex with MI329 -

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Basic information

Entry
Database: PDB / ID: 3rly
TitleHuman Thrombin in complex with MI329
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


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 / 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 / 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
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 / 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
N-(BENZYLSULFONYL)-D-ALANYL-N-(4-CARBAMIMIDOYLBENZYL)-L-PROLINAMIDE / PHOSPHATE ION / Chem-S29 / Prothrombin / Hirudin variant-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsBiela, A. / Heine, A. / Klebe, G.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Ligand binding stepwise disrupts water network in thrombin: enthalpic and entropic changes reveal classical hydrophobic effect
Authors: Biela, A. / Sielaff, F. / Terwesten, F. / Heine, A. / Steinmetzer, T. / Klebe, G.
History
DepositionApr 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other
Revision 1.2Jul 13, 2016Group: Database references
Revision 1.3Jul 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 1.4Nov 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 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 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
L: Thrombin Light Chain
H: Thrombin Heavy Chain
I: Hirudin variant-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,93710
Polymers35,5393
Non-polymers1,3977
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-12 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.300, 71.400, 72.400
Angle α, β, γ (deg.)90.00, 100.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-1070-

HOH

21H-1331-

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 , 5 types, 353 molecules

#5: Chemical ChemComp-S29 / N-(benzylsulfonyl)-D-alanyl-N-(4-carbamimidoylbenzyl)-L-prolinamide


Type: peptide-like, Peptide-like / Class: Thrombin inhibitor / Mass: 471.572 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H29N5O4S
References: N-(BENZYLSULFONYL)-D-ALANYL-N-(4-CARBAMIMIDOYLBENZYL)-L-PROLINAMIDE
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 2009 / Details: Collimating mirror
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. all: 55139 / Num. obs: 55139 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 12.89 Å2 / Rsym value: 0.051 / Net I/σ(I): 24.8
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 2742 / Rsym value: 0.487 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H8D

1h8d


Resolution: 1.51→35.617 Å / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.9124 / SU ML: 0.16 / Cross valid method: Free R / σ(F): 0 / Phase error: 15.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1715 2659 5.04 %Random
Rwork0.1547 ---
all0.1555 55377 --
obs0.1555 52718 95.43 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.792 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso max: 84.8 Å2 / Biso mean: 21.1242 Å2 / Biso min: 6.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.3278 Å20 Å2-3.2716 Å2
2---2.0029 Å20 Å2
3----0.3249 Å2
Refinement stepCycle: LAST / Resolution: 1.51→35.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 93 347 2784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092616
X-RAY DIFFRACTIONf_angle_d1.1143561
X-RAY DIFFRACTIONf_chiral_restr0.075368
X-RAY DIFFRACTIONf_plane_restr0.005452
X-RAY DIFFRACTIONf_dihedral_angle_d17.7411048
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5101-1.56410.24052560.21554539479587
1.5641-1.62670.23092520.18624674492690
1.6267-1.70070.18692620.16794806506892
1.7007-1.79040.16472820.15134968525095
1.7904-1.90260.16052990.14194942524196
1.9026-2.04940.16442490.13975113536298
2.0494-2.25560.17532500.1445253550399
2.2556-2.5820.1832730.15295190546399
2.582-3.25270.17662710.16415244551599
3.2527-35.62650.14932650.1495330559599
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)
11.2734-0.80180.26730.7913-0.03240.12960.20730.3178-0.2196-0.2063-0.15540.12920.1055-0.041-0.04350.12710.046-0.02590.1392-0.04830.10827.7273-2.084912.2417
21.1955-0.51130.21191.7106-0.14720.11440.26830.4387-0.0146-0.4265-0.2577-0.08270.08290.17290.0180.16720.07720.00750.18050.0030.090716.24791.99210.2869
31.2517-0.62020.27461.045-0.09290.78090.19370.30320.043-0.1675-0.1937-0.1160.07190.1610.00840.10030.06030.01550.15420.00560.074418.8414-0.218412.1229
41.3445-0.3565-0.07861.06990.5540.305-0.1348-0.23790.00120.23460.2009-0.08410.03310.1125-0.03630.12770.0356-0.01940.1327-0.02720.10419.90934.965133.3032
53.8091-0.27892.57240.10160.15733.72090.33760.2096-0.7162-0.28450.03410.33070.4574-0.027-0.34270.1660.0212-0.07520.1136-0.06590.22393.941-9.937214.3779
61.0334-0.64840.21740.6133-0.13540.6303-0.0012-0.0958-0.17230.09710.04770.10270.0987-0.015-0.03090.10280.01310.01170.07470.00680.098910.8245-5.132829.4904
72.20361.5587-3.34812.8576-3.20295.71240.1961-0.04450.52870.0601-0.0567-0.3999-0.48660.4337-0.1220.1593-0.02920.03940.16340.01380.306527.1098.889821.8626
82.33951.0841-0.24563.0684-1.35070.65970.19250.9762-0.2212-0.8188-0.1464-0.0680.0039-0.2546-0.03850.4130.18110.0370.5158-0.11740.112912.0734-1.5308-3.4787
92.1746-0.0510.49540.0097-0.00041.5829-0.160.1180.44130.0283-0.0179-0.3944-0.5350.17110.14350.185-0.0073-0.01030.1090.03130.198410.06916.734719.5677
100.7856-0.6292-0.2031.12150.38710.30340.0867-0.0419-0.0229-0.1488-0.16670.0097-0.0939-0.09930.05760.11410.06620.01040.1052-0.0090.0997-0.867114.506817.6045
110.7224-0.84170.14141.00770.01151.18320.0096-0.1665-0.19020.09020.10130.2639-0.0014-0.4163-0.05040.10050.02610.01860.16350.00310.1576-2.7037.19928.075
120.8656-0.08811.08421.26190.1091.41950.0229-0.2367-0.12050.00840.10420.00560.0427-0.2619-0.05520.13390.02450.05140.13590.0060.1508-0.11364.795933.9586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 16:37)
2X-RAY DIFFRACTION2(chain H and resid 38:50)
3X-RAY DIFFRACTION3(chain H and resid 51:125)
4X-RAY DIFFRACTION4(chain H and resid 126:138)
5X-RAY DIFFRACTION5(chain H and resid 139:156)
6X-RAY DIFFRACTION6(chain H and resid 157:232)
7X-RAY DIFFRACTION7(chain H and resid 233:246)
8X-RAY DIFFRACTION8(chain I and resid 55:65)
9X-RAY DIFFRACTION9(chain L and resid 1C:3)
10X-RAY DIFFRACTION10(chain L and resid 4:12)
11X-RAY DIFFRACTION11(chain L and resid 13:14D)
12X-RAY DIFFRACTION12(chain L and resid 14E:14K)

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