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- PDB-1sr5: ANTITHROMBIN-ANHYDROTHROMBIN-HEPARIN TERNARY COMPLEX STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1sr5
TitleANTITHROMBIN-ANHYDROTHROMBIN-HEPARIN TERNARY COMPLEX STRUCTURE
Components
  • (Prothrombin) x 2
  • Antithrombin-III
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE INHIBITOR / ANTITHROMBIN ACTIVATION BY HEP ANHYDROTHROMBIN / PROTEIN-PROTEIN INTERACTIONS / 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 / 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 / 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 / Post-translational protein phosphorylation / 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 / 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 / protease binding / 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 / identical protein binding / plasma membrane
Similarity search - Function
Antithrombin-III, serpin domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain ...Antithrombin-III, serpin domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / 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 / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
heparin heptasaccharide / 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose / Prothrombin / Antithrombin-III
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsDementiev, A. / Petitou, M. / Gettins, P.G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: The ternary complex of antithrombin-anhydrothrombin-heparin reveals the basis of inhibitor specificity.
Authors: Dementiev, A. / Petitou, M. / Herbert, J.M. / Gettins, P.G.
History
DepositionMar 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Sep 24, 2014Group: Database references
Revision 2.0Apr 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Aug 23, 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
Remark 600HETEROGEN The hetgroups NT1 and NT2 in the coordinates represent the visible in the electron ...HETEROGEN The hetgroups NT1 and NT2 in the coordinates represent the visible in the electron density parts of heparin hexadecasaccharide (C129O132S17H201). J.M. HERBERT, J.P.HERAULT, A.BERNAT, P.SAVI, P.SCHAEFFER, P.A.DRIGUES, P.DUCHAUSSOY, M.PETITOU. "SR123782A, A SYNTHETIC HEPARIN MIMETIC". THROMB.HAEMOST., V.85, PP.852-860.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antithrombin-III
B: Prothrombin
C: Prothrombin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9588
Polymers82,9783
Non-polymers2,9805
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-15 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.040, 90.700, 159.900
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 , 2 types, 2 molecules AC

#1: Protein Antithrombin-III / ATIII / PRO0309


Mass: 49101.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLASMA / References: UniProt: P01008
#3: Protein Prothrombin / Coagulation factor II


Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: heavy chain (residues 364-622) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLASMA / References: UniProt: P00734, thrombin

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Protein/peptide / Non-polymers , 2 types, 76 molecules B

#2: Protein/peptide Prothrombin / Coagulation factor II


Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: light chain (residues 328-363) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLASMA / References: UniProt: P00734, thrombin
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 3 types, 5 molecules

#4: Polysaccharide 4-deoxy-2,3,6-tri-O-methyl-alpha-D-xylo-hexopyranose-(1-4)-2,3,6-tri-O-methyl-beta-D-glucopyranose- ...4-deoxy-2,3,6-tri-O-methyl-alpha-D-xylo-hexopyranose-(1-4)-2,3,6-tri-O-methyl-beta-D-glucopyranose-(1-4)-2,3-di-O-methyl-6-O-sulfo-alpha-D-glucopyranose-(1-4)-(2R,3R,4S,5S,6S)-6-(dihydroxymethyl)-3,4-dimethoxytetrahydro-2H-pyran-2,5-diol-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-(2R,3R,4S,5S,6R)-6-(dihydroxymethyl)-3,4-dimethoxytetrahydro-2H-pyran-2,5-diol-(1-4)-1,5-anhydro-3-O-methyl-2,6-di-O-sulfo-D-glucitol / heparin heptasaccharide


Type: oligosaccharide, Oligosaccharide / Class: Anticoagulant / Mass: 1815.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: heparin heptasaccharide
DescriptorTypeProgram
[][D-1-deoxy-Glcp2SO33Me6SO3]{[(4+1)][a-L-IdopA2Me3Me]{[(4+1)][a-D-Glcp2SO33SO36SO3]{[(4+1)][b-D-GlcpA2Me3Me]{[(4+1)][a-D-Glcp2Me3Me6SO3]{[(4+1)][b-D-6-deoxy-Glcp2Me3Me]{[(4+1)][a-D-4,6-deoxy-Glcp2Me3Me]{}}}}}}}LINUCSPDB-CARE
#5: 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.: 3
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
#6: Sugar ChemComp-GU4 / 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose / 2,3,4,6-tetra-O-sulfonato-alpha-D-glucose / 2,3,4,6-tetra-O-sulfonato-D-glucose / 2,3,4,6-tetra-O-sulfonato-glucose


Type: D-saccharide, alpha linking / Mass: 500.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O18S4
IdentifierTypeProgram
DGlcp[2S,3S,4S,6S]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
2-sulfo-3-sulfo-4-sulfo-6-sulfo-a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-Glcp2SO33SO34SO36SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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: 3.6 Å3/Da / Density % sol: 65 %
Description: The structure factor file contains Friedel pairs.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: PEG 3350, tri-sodium citrate, pH 8.40, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 19, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 3.1→40 Å / Num. obs: 24227 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.3
Reflection shellResolution: 3.08→3.27 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.56 / % possible all: 86.8

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AZX, PDB ENTRY 1JMO

1azx

1jmo


Resolution: 3.1→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 137693.49 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Friedel pairs were used.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2278 5 %RANDOM
Rwork0.227 ---
all-45659 --
obs-45659 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.9201 Å2 / ksol: 0.233916 e/Å3
Displacement parametersBiso mean: 62 Å2
Baniso -1Baniso -2Baniso -3
1--19.43 Å20 Å20 Å2
2--51.65 Å20 Å2
3----32.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.92 Å0.89 Å
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5293 0 166 75 5534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 368 4.9 %
Rwork0.403 7189 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.PARAM
X-RAY DIFFRACTION3NAG.PARNAG.TOP
X-RAY DIFFRACTION4NTP.PARNTP.TOP

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