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- PDB-3rlw: Human Thrombin in complex with MI328 -

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Basic information

Entry
Database: PDB / ID: 3rlw
TitleHuman Thrombin in complex with MI328
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 / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / regulation of cytosolic calcium ion concentration / 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)GLYCYL-N-(4-CARBAMIMIDOYLBENZYL)-L-PROLINAMIDE / PHOSPHATE ION / Chem-S28 / Prothrombin / Hirudin variant-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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 / pdbx_struct_special_symmetry / 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 1.6Nov 13, 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)36,63511
Polymers35,5393
Non-polymers1,0968
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-14 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.500, 71.300, 72.500
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-1173-

HOH

31H-1194-

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, 248 molecules

#5: Chemical ChemComp-S28 / N-(benzylsulfonyl)glycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide


Type: peptide-like, Peptide-like / Class: Thrombin inhibitor / Mass: 457.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N5O4S
References: N-(BENZYLSULFONYL)GLYCYL-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.: 3 / 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.: 241 / 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: 51.19 %
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: 1.69→50 Å / Num. all: 38822 / Num. obs: 38822 / % possible obs: 97.7 % / Redundancy: 2.5 % / Biso Wilson estimate: 15.82 Å2 / Rsym value: 0.059 / Net I/σ(I): 14.6
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2 / Num. unique all: 1961 / Rsym value: 0.49 / % possible all: 98.8

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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: 1.69→34.648 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8947 / SU ML: 0.16 / Cross valid method: Free R / σ(F): 0 / Phase error: 17.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1826 5.01 %Random
Rwork0.1626 ---
all0.1641 38269 --
obs0.1641 36443 92.13 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.279 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso max: 93.64 Å2 / Biso mean: 24.1118 Å2 / Biso min: 7.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.044 Å20 Å2-2.8331 Å2
2---1.6085 Å20 Å2
3----0.4355 Å2
Refinement stepCycle: LAST / Resolution: 1.69→34.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 0 71 241 2663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082552
X-RAY DIFFRACTIONf_angle_d1.063461
X-RAY DIFFRACTIONf_chiral_restr0.074355
X-RAY DIFFRACTIONf_plane_restr0.005439
X-RAY DIFFRACTIONf_dihedral_angle_d17.9281017
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 (%)
1.69-1.75040.29211770.22423084326183
1.7504-1.82050.21481710.18523247341887
1.8205-1.90330.20111680.17253296346488
1.9033-2.00370.21042050.16493477368293
2.0037-2.12920.1821990.15683563376296
2.1292-2.29360.17961760.15533593376995
2.2936-2.52430.2051830.16263590377396
2.5243-2.88940.22761810.1783599378096
2.8894-3.63970.17052080.15773602381096
3.6397-34.65570.16961580.14963566372492
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)
11.4192-0.86610.38080.9647-0.11310.75420.2770.3354-0.0368-0.2169-0.249-0.04790.10120.149-0.00990.12980.0780.00090.1545-0.00790.072916.3795-0.839711.6509
20.6923-0.3739-0.36490.64730.34090.2401-0.0172-0.15460.10710.12650.0898-0.0061-0.03430.1035-0.03980.13510.0231-0.01450.1401-0.01610.104511.00366.578430.9666
31.845-0.59340.91780.2934-0.03291.31370.22380.2182-0.6125-0.3710.13310.32540.1628-0.057-0.26750.1790.0266-0.09070.1217-0.06940.22163.8666-9.971114.4145
40.3077-0.4553-0.1280.72150.05430.3514-0.0933-0.1503-0.10210.19740.09650.08190.04980.0301-0.00280.1480.01930.00340.11160.02290.132913.264-2.9726.837
51.61991.4773-0.95512.534-0.43591.2524-0.55340.10240.06490.06140.20460.28040.327-0.13630.14540.29130.010.10570.31540.2140.4924-0.3091-11.641535.9165
61.3447-0.72350.09580.4798-0.15990.71450.0254-0.0659-0.1937-0.00960.01910.0930.12470.0304-0.00120.09240.01640.00520.07030.00060.087911.155-2.213526.4095
70.39280.78340.1982.7555-1.26222.53790.2360.05190.2670.1824-0.0631-0.5797-0.36740.4828-0.13740.2109-0.03840.04460.21790.02540.354428.319.987720.0155
81.6623-0.4299-0.17191.0991-0.36760.23960.39981.124-0.161-0.9792-0.2644-0.1320.1894-0.0652-0.13510.53710.23550.02190.6233-0.08990.150311.9321-1.7131-3.5692
90.7341-1.17240.13151.9183-0.57893.0154-0.09980.1280.2767-0.1088-0.0684-0.8849-0.5249-0.06260.1090.17410.00790.0090.11110.01560.23099.807116.778619.736
100.4153-0.1221-0.05070.30480.10720.11690.06-0.14540.1285-0.0921-0.10890.0989-0.0018-0.14840.05220.12890.07060.02140.1288-0.00240.1093-1.492514.106818.2566
110.1292-0.0679-0.37320.5278-0.31222.11490.0515-0.1288-0.08070.10520.17550.199-0.0208-0.4431-0.16260.120.03550.03420.15290.01110.1582-2.18815.182930.1081
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain H and resid 16:119)H16 - 119
2X-RAY DIFFRACTION2(chain H and resid 120:138)H120 - 138
3X-RAY DIFFRACTION3(chain H and resid 139:156)H139 - 156
4X-RAY DIFFRACTION4(chain H and resid 157:184A)H157 - 184
5X-RAY DIFFRACTION5(chain H and resid 185:186D)H185 - 186
6X-RAY DIFFRACTION6(chain H and resid 187:235)H187 - 235
7X-RAY DIFFRACTION7(chain H and resid 236:246)H236 - 246
8X-RAY DIFFRACTION8(chain I and resid 55:65)I55 - 65
9X-RAY DIFFRACTION9(chain L and resid 1C:3)L1 - 3
10X-RAY DIFFRACTION10(chain L and resid 4:13)L4 - 13
11X-RAY DIFFRACTION11(chain L and resid 14:14K)L14

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