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- PDB-3rml: Human Thrombin in complex with MI331 -

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Basic information

Entry
Database: PDB / ID: 3rml
TitleHuman Thrombin in complex with MI331
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 / Hirudin / Blood / glycosylation / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / 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 / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / 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 / Golgi lumen / positive regulation of protein localization to nucleus / 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 / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Thrombin inhibitor hirudin / Hirudin / Proteinase inhibitor I14, hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle ...Thrombin inhibitor hirudin / Hirudin / Proteinase inhibitor I14, 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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-[2-(AMINOMETHYL)-5-CHLOROBENZYL]-L-PROLINAMIDE / Chem-M31 / PHOSPHATE ION / Prothrombin / Hirudin variant-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 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 21, 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

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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)36,56510
Polymers35,5393
Non-polymers1,0257
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-14 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.300, 71.200, 72.400
Angle α, β, γ (deg.)90.00, 99.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-1030-

HOH

21H-1253-

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 / N-Acetylglucosamine


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, 303 molecules

#5: Chemical ChemComp-M31 / N-(benzylsulfonyl)glycyl-N-[2-(aminomethyl)-5-chlorobenzyl]-L-prolinamide


Type: peptide-like, Peptide-like / Class: Thrombin inhibitor / Mass: 478.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27ClN4O4S
References: N-(BENZYLSULFONYL)GLYCYL-N-[2-(AMINOMETHYL)-5-CHLOROBENZYL]-L-PROLINAMIDE
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


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 / Water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.31 %
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: 108 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: 1.53→50 Å / Num. all: 50478 / Num. obs: 50478 / % possible obs: 96.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 14.43 Å2 / Rsym value: 0.035 / Net I/σ(I): 29.2
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 2436 / Rsym value: 0.357 / % possible all: 92.2

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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: 1.53→35.661 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.8904 / SU ML: 0.17 / Cross valid method: Free R / σ(F): 0 / Phase error: 18.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1856 2389 4.99 %Random
Rwork0.1587 ---
all0.16 50305 --
obs0.16 47916 91.6 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.984 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 91.76 Å2 / Biso mean: 24.4019 Å2 / Biso min: 7.79 Å2
Baniso -1Baniso -2Baniso -3
1-3.3799 Å20 Å2-3.0716 Å2
2---2.441 Å20 Å2
3----0.939 Å2
Refinement stepCycle: LAST / Resolution: 1.53→35.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 65 297 2702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092542
X-RAY DIFFRACTIONf_angle_d1.0833453
X-RAY DIFFRACTIONf_chiral_restr0.075357
X-RAY DIFFRACTIONf_plane_restr0.005438
X-RAY DIFFRACTIONf_dihedral_angle_d17.0321006
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 (%)
1.53-1.58470.24021870.22043968415580
1.5847-1.64820.24562180.19984140435883
1.6482-1.72320.21972130.17864241445486
1.7232-1.8140.19662260.15614390461689
1.814-1.92770.17162340.15354519475391
1.9277-2.07650.17212540.14984700495495
2.0765-2.28540.16722490.15314830507998
2.2854-2.61610.18752650.16024904516999
2.6161-3.29560.21772890.16524905519499
3.2956-35.67060.16192540.14684930518498
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)
11.4748-0.77490.79890.7438-0.55350.65910.37160.453-0.1147-0.276-0.3076-0.00330.2330.2148-0.05570.18210.1242-0.01830.2103-0.03590.095713.776-0.64320.12
21.4397-0.217-0.4980.16950.36680.85940.23440.3745-0.0616-0.3262-0.461-0.1223-0.0637-0.18340.18690.45040.42020.04310.73570.00870.174516.84-10.54124.92
31.6719-0.8530.61541.1675-0.23680.92290.20950.29230.0407-0.1658-0.1991-0.05680.09820.2086-0.01360.11170.06870.00240.1343-0.00380.049314.37972.773215.9184
41.0591-0.91930.04771.1714-0.51160.58910.0402-0.0936-0.19570.06360.01760.15270.1352-0.0126-0.06060.14760.0022-0.0180.0950.00060.118311.2936-7.039229.4405
53.41251.7839-0.85611.3460.49613.109-0.1278-0.1076-0.12960.18710.27780.1040.6076-0.3358-0.06850.3079-0.02750.0140.23670.13810.3494-0.2981-10.29335.479
61.2375-0.52080.34060.3352-0.30221.24680.13490.0055-0.17-0.078-0.06390.09010.18940.0192-0.06330.11910.0389-0.00980.0918-0.00780.101910.3891-1.721226.093
71.24311.0552-1.90412.4625-2.34514.52520.2346-0.06580.61310.1079-0.1044-0.4448-0.41970.5798-0.0410.1631-0.00580.0540.22730.05810.354827.05679.813321.79
81.60140.27110.32441.1408-0.13070.10430.30960.8918-0.0667-0.865-0.2135-0.04590.17580.1957-0.09820.56520.31240.03540.6215-0.10520.128811.9189-0.5434-3.4133
91.3514-1.07370.26491.0854-0.41470.70240.04970.03180.2288-0.0132-0.179-0.1109-0.3015-0.03690.06390.15910.06190.00710.1302-0.00350.12773.018516.243218.371
100.96580.21670.43650.06780.08920.20120.1088-0.1192-0.1262-0.039-0.1149-0.01980.0807-0.17550.0120.0950.0427-0.00560.1649-0.00860.156-2.828.50727.605
112.6783-1.44561.60651.6807-0.68851.21010.0907-0.38990.02160.09630.05970.2256-0.3531-0.617-0.14120.15790.04260.04990.20670.010.1586-1.02166.324233.2951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 16:60H)
2X-RAY DIFFRACTION2(chain H and resid 60I:64)
3X-RAY DIFFRACTION3(chain H and resid 65:146)
4X-RAY DIFFRACTION4(chain H and resid 147:184A)
5X-RAY DIFFRACTION5(chain H and resid 185:186D)
6X-RAY DIFFRACTION6(chain H and resid 187:232)
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:11)
10X-RAY DIFFRACTION10(chain L and resid 12:14C)
11X-RAY DIFFRACTION11(chain L and resid 14D:14K)

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