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- PDB-3u9a: Human Thrombin In Complex With MI330 -

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Basic information

Entry
Database: PDB / ID: 3u9a
TitleHuman Thrombin In Complex With MI330
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)-N-[[2-(AMINOMETHYL)-5-CHLORANYL-PHENYL]METHYL]-1-[(2S)-2-[(3-CHLORANYL-4-METHOXY-PHENYL)SULFONYLAMINO]-4-[(4-CYANOPHENYL)METHYLAMINO]-4-OXIDANYLIDENE-BUTANOYL]PYRROLIDINE-2-CARBOXAMIDE / PHOSPHATE ION / Chem-S33 / Prothrombin / Hirudin variant-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 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
L: Thrombin Light Chain
H: Thrombin Heavy Chain
I: Hirudin variant-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,78710
Polymers35,5393
Non-polymers1,2487
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-37 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.900, 71.200, 72.600
Angle α, β, γ (deg.)90.00, 100.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-75-

ARG

21H-1195-

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, 259 molecules

#5: Chemical ChemComp-S33 / (2S)-N-[[2-(aminomethyl)-5-chloranyl-phenyl]methyl]-1-[(2S)-2-[(3-chloranyl-4-methoxy-phenyl)sulfonylamino]-4-[(4-cyanophenyl)methylamino]-4-oxidanylidene-butanoyl]pyrrolidine-2-carboxamide


Type: Peptide-like / Class: Thrombin inhibitor / Mass: 701.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H34Cl2N6O6S
References: (2S)-N-[[2-(AMINOMETHYL)-5-CHLORANYL-PHENYL]METHYL]-1-[(2S)-2-[(3-CHLORANYL-4-METHOXY-PHENYL)SULFONYLAMINO]-4-[(4-CYANOPHENYL)METHYLAMINO]-4-OXIDANYLIDENE-BUTANOYL]PYRROLIDINE-2-CARBOXAMIDE
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#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.: 253 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
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: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2009 / Details: Collimating Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. all: 46917 / Num. obs: 46917 / % possible obs: 97.6 % / Redundancy: 3 % / Biso Wilson estimate: 17.32 Å2 / Rsym value: 0.037 / Net I/σ(I): 28.8
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 2328 / Rsym value: 0.471 / % possible all: 95.6

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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: 1.58→35.737 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8887 / SU ML: 0.2 / Cross valid method: Free R / σ(F): 0 / Phase error: 18.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1957 2233 4.97 %Random
Rwork0.1638 ---
all0.1653 47166 --
obs0.1653 44933 93.55 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.821 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 94.91 Å2 / Biso mean: 26.0604 Å2 / Biso min: 9.06 Å2
Baniso -1Baniso -2Baniso -3
1-2.9464 Å20 Å2-4.0143 Å2
2---3.6478 Å2-0 Å2
3---0.7014 Å2
Refinement stepCycle: LAST / Resolution: 1.58→35.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 80 253 2667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082559
X-RAY DIFFRACTIONf_angle_d1.0873480
X-RAY DIFFRACTIONf_chiral_restr0.074359
X-RAY DIFFRACTIONf_plane_restr0.005440
X-RAY DIFFRACTIONf_dihedral_angle_d17.4321013
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.61440.28171130.2332377249083
1.6144-1.65190.23181420.22472408255085
1.6519-1.69320.27211380.20812459259787
1.6932-1.7390.21151240.19892478260287
1.739-1.79020.23381310.18132591272290
1.7902-1.8480.18921250.17672629275492
1.848-1.9140.21741410.16292619276093
1.914-1.99060.17511660.15522664283095
1.9906-2.08120.18941510.15292745289696
2.0812-2.19090.16791100.15562784289497
2.1909-2.32820.19891630.15822780294398
2.3282-2.50790.19311380.16162846298499
2.5079-2.76020.20681630.1772813297699
2.7602-3.15940.20341480.1682825297399
3.1594-3.97970.16231320.14742846297899
3.9797-35.74660.19821480.15582836298497
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)
10.8018-0.46960.19490.4508-0.08860.37530.49550.7028-0.1663-0.5688-0.29750.18220.31440.08150.29280.19360.20230.02230.2515-0.11050.035613.7266-0.46939.6254
20.4149-0.09710.06840.28830.10280.20390.0860.12360.14180.0014-0.104-0.1695-0.03720.12320.01110.14170.0587-0.00010.18090.01610.142220.59734.454719.4784
30.5847-0.48280.06830.4349-0.22080.33090.0865-0.0259-0.2840.0122-0.0050.23850.1979-0.0068-0.04640.17280.0198-0.01540.11840.0030.16288.6607-6.230227.0726
40.4180.0879-0.38890.2580.08410.5726-0.042-0.2044-0.26230.16860.1610.25030.1712-0.0615-0.02370.1945-0.00510.00960.16910.07720.24989.202-6.49633.5
50.5269-0.23170.08840.1249-0.09330.37170.0458-0.0744-0.16010.025-0.01720.05950.1042-0.00190.00250.10660.02670.00230.0892-0.00370.129712.0693-0.355726.2072
60.07170.04290.09920.2718-0.11870.26680.07860.0780.12520.0043-0.008-0.1189-0.10920.0619-0.0230.2607-0.02110.07580.2640.07150.459829.279912.454218.2972
70.0564-0.0119-0.05740.02740.00940.06040.0940.08060.0178-0.0512-0.0117-0.0211-0.02870.00460.05960.50240.27620.07430.5718-0.15150.076112.002-0.5325-3.2107
80.47920.0371-0.52750.0088-0.04150.5803-0.01570.01870.2335-0.0572-0.0611-0.161-0.19380.05070.03220.20410.02620.01350.13430.02810.22789.766617.898919.713
90.806-0.16690.16410.53690.03470.0890.0757-0.0681-0.0194-0.1333-0.08260.0419-0.0454-0.11930.0340.15640.06550.0040.176-0.0220.171-2.453512.440819.8516
100.1884-0.03210.1250.07390.05250.17330.0369-0.13070.05370.0314-0.03420.0737-0.0582-0.20960.01280.16330.04190.05760.22610.01030.1953-0.50525.967133.614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain H and resid 16:85)H16 - 85
2X-RAY DIFFRACTION2(chain H and resid 86:129C)H86 - 129
3X-RAY DIFFRACTION3(chain H and resid 130:176)H130 - 176
4X-RAY DIFFRACTION4(chain H and resid 177:186D)H177 - 186
5X-RAY DIFFRACTION5(chain H and resid 187:238)H187 - 238
6X-RAY DIFFRACTION6(chain H and resid 239:246)H239 - 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 4:14C)L4 - 14
10X-RAY DIFFRACTION10(chain L and resid 14D:14K)L14

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