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- PDB-5l6n: Disulfated madanin-thrombin complex -

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Basic information

Entry
Database: PDB / ID: 5l6n
TitleDisulfated madanin-thrombin complex
Components
  • (Prothrombin) x 2
  • Thrombin inhibitor madanin 1
KeywordsHYDROLASE / Anticoagulant Sulfotyrosine
Function / homology
Function and homology information


molecular function inhibitor activity / 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 / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway ...molecular function inhibitor activity / 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 / 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 / acute-phase response / Regulation of Complement cascade / 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 / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / 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
Thrombin inhibitor Madanin / Thrombin inhibitor Madanin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily ...Thrombin inhibitor Madanin / Thrombin inhibitor Madanin / 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
Prothrombin / Thrombin inhibitor madanin 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Haemaphysalis longicornis (longhorned tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.627 Å
AuthorsRipoll-Rozada, J. / Pereira, P.J.B.
CitationJournal: Nat Chem / Year: 2017
Title: Tyrosine sulfation modulates activity of tick-derived thrombin inhibitors.
Authors: Thompson, R.E. / Liu, X. / Ripoll-Rozada, J. / Alonso-Garcia, N. / Parker, B.L. / Pereira, P.J.B. / Payne, R.J.
History
DepositionMay 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 1.3Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Prothrombin
H: Prothrombin
I: Thrombin inhibitor madanin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1515
Polymers37,9073
Non-polymers2442
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-23 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.546, 80.238, 91.369
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 2 types, 2 molecules LI

#1: Protein/peptide Prothrombin / Coagulation factor II


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 Thrombin inhibitor madanin 1


Mass: 4030.206 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Haemaphysalis longicornis (longhorned tick)
References: UniProt: Q86FP9

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Protein / Sugars , 2 types, 2 molecules H

#2: Protein Prothrombin / Coagulation factor II


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 , 2 types, 234 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MMT buffer pH 7.0, 30% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.627→44.55 Å / Num. obs: 41771 / % possible obs: 99.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.6
Reflection shellResolution: 1.63→1.71 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U69

3u69


Resolution: 1.627→39.701 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1985 2144 5.14 %
Rwork0.1666 --
obs0.1682 41712 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.627→39.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 15 233 2729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092586
X-RAY DIFFRACTIONf_angle_d0.8983496
X-RAY DIFFRACTIONf_dihedral_angle_d22.4381559
X-RAY DIFFRACTIONf_chiral_restr0.058365
X-RAY DIFFRACTIONf_plane_restr0.006452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6267-1.66450.25891280.26922564X-RAY DIFFRACTION97
1.6645-1.70610.28141440.25532584X-RAY DIFFRACTION100
1.7061-1.75230.28331570.24512600X-RAY DIFFRACTION100
1.7523-1.80380.27041480.22442575X-RAY DIFFRACTION100
1.8038-1.86210.26331500.20642634X-RAY DIFFRACTION100
1.8621-1.92860.22881430.1882604X-RAY DIFFRACTION100
1.9286-2.00580.21621460.17782610X-RAY DIFFRACTION100
2.0058-2.09710.23581340.17492618X-RAY DIFFRACTION100
2.0971-2.20770.18891400.15782638X-RAY DIFFRACTION100
2.2077-2.3460.20191270.16622672X-RAY DIFFRACTION100
2.346-2.52710.1891450.16872626X-RAY DIFFRACTION100
2.5271-2.78130.20821480.16662671X-RAY DIFFRACTION100
2.7813-3.18360.19661520.17042659X-RAY DIFFRACTION100
3.1836-4.01040.17791450.14322694X-RAY DIFFRACTION99
4.0104-39.71240.15991370.14332819X-RAY DIFFRACTION99
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)
13.14841.1177-1.75277.1908-1.93632.0509-0.0454-0.27360.08480.20030.12240.56190.0856-0.6069-0.1070.18490.01660.06050.1909-0.00970.2044-2.144310.925230.9735
22.4605-0.5141-2.06353.9777-0.52045.8779-0.0422-0.90240.4290.5414-0.02280.1759-0.4205-0.13910.00410.2965-0.02110.0460.2649-0.05710.14353.413312.743537.4586
36.79270.88942.70722.5788-1.41452.69660.307-0.58730.7870.4785-0.2339-0.4633-1.22620.6651-0.21770.4139-0.07650.05450.2755-0.12630.343713.28321.404931.2157
41.70540.3719-0.35861.41230.12072.352-0.05490.0876-0.1983-0.04490.0046-0.09910.31130.05810.05180.18560.00810.02090.1427-0.00680.17527.4717-2.21917.6374
52.96390.0075-0.80842.24461.08876.0072-0.1106-0.0961-0.21320.1047-0.080.05930.7007-0.12930.13630.2932-0.01950.04880.112-0.00160.22322.3715-8.327526.0732
62.01130.2427-0.44362.0245-0.12012.6198-0.04550.2396-0.0505-0.1918-0.03690.12650.1283-0.22470.07030.1576-0.0026-0.01120.1666-0.00230.13891.94722.55212.7084
72.8985-0.8542-0.19342.9767-0.0821.20760.1430.11790.4381-0.1647-0.0679-0.2251-0.32920.0059-0.07020.21530.00020.05490.14640.00990.18349.947819.090920.9891
81.6080.1975-2.61393.024-1.00534.4243-0.6372-0.6538-1.10050.0172-0.1066-0.3350.59570.91740.62930.24910.08190.04850.3070.06910.315319.1488-4.059826.5233
92.3236-0.1842-0.59211.54340.38391.91180.07630.05190.202-0.08420.0293-0.2528-0.19290.3096-0.08210.141-0.02430.03520.1488-0.00020.181617.360912.131218.2873
102.1143.7284-0.66457.3210.4395.7224-0.1590.70370.5045-0.48760.2150.8019-0.0219-0.99930.00550.23280.0752-0.0510.39810.04880.2672-2.932710.29927.7086
112.23081.1274-0.51542.47361.74822.24070.21860.61320.0721-1.723-0.34490.9088-0.4813-1.62050.03670.64460.0675-0.11070.64330.15410.46013.463215.97861.0343
122.46870.4204-2.26284.99270.78762.49820.22290.58460.1178-0.8325-0.31940.5103-0.7528-0.86780.0960.9620.4365-0.05751.2521-0.16620.5419.66428.1645-7.0019
134.16111.2734-1.40391.1182-0.01163.4348-0.38890.4978-0.139-0.46630.2024-0.0710.18070.18320.20320.3094-0.03470.03350.3234-0.00460.225122.77133.75942.2814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 291 through 299 )
2X-RAY DIFFRACTION2chain 'L' and (resid 300 through 308 )
3X-RAY DIFFRACTION3chain 'L' and (resid 309 through 319 )
4X-RAY DIFFRACTION4chain 'H' and (resid 321 through 375 )
5X-RAY DIFFRACTION5chain 'H' and (resid 376 through 396 )
6X-RAY DIFFRACTION6chain 'H' and (resid 397 through 442 )
7X-RAY DIFFRACTION7chain 'H' and (resid 443 through 460 )
8X-RAY DIFFRACTION8chain 'H' and (resid 461 through 480 )
9X-RAY DIFFRACTION9chain 'H' and (resid 481 through 563 )
10X-RAY DIFFRACTION10chain 'H' and (resid 564 through 579 )
11X-RAY DIFFRACTION11chain 'I' and (resid 31 through 37 )
12X-RAY DIFFRACTION12chain 'I' and (resid 38 through 42 )
13X-RAY DIFFRACTION13chain 'I' and (resid 43 through 54 )

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