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- PDB-1azx: ANTITHROMBIN/PENTASACCHARIDE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1azx
TitleANTITHROMBIN/PENTASACCHARIDE COMPLEX
ComponentsANTITHROMBIN
KeywordsSERINE PROTEASE INHIBITOR / SERPIN / ANTITHROMBIN / ANTICOAGULANT ACTIVATION BY HEPARIN
Function / homology
Function and homology information


regulation of blood coagulation / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / heparin binding / collagen-containing extracellular matrix / blood microparticle ...regulation of blood coagulation / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / heparin binding / collagen-containing extracellular matrix / blood microparticle / protease binding / endoplasmic reticulum lumen / 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 / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
heparin pentasaccharide / Antithrombin-III
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJin, L. / Abrahams, J.P. / Skinner, R. / Petitou, M. / Pike, R.N. / Carrell, R.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: The anticoagulant activation of antithrombin by heparin.
Authors: Jin, L. / Abrahams, J.P. / Skinner, R. / Petitou, M. / Pike, R.N. / Carrell, R.W.
History
DepositionNov 23, 1997Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_struct_assembly_gen / 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.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: ANTITHROMBIN
L: ANTITHROMBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1887
Polymers98,2022
Non-polymers3,9865
Water0
1
L: ANTITHROMBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2054
Polymers49,1011
Non-polymers2,1043
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
I: ANTITHROMBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9843
Polymers49,1011
Non-polymers1,8832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.440, 86.970, 97.220
Angle α, β, γ (deg.)90.00, 108.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ANTITHROMBIN /


Mass: 49101.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PENTASACCHARIDE WAS CHEMICALLY SYNTHESIZED / Source: (natural) Homo sapiens (human) / Organ: PLASMA / Tissue: PLASMA / References: UniProt: P01008
#2: Polysaccharide 3,4-di-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranose-(1-4)-2,3-di-O-methyl-beta-D-glucopyranuronic ...3,4-di-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranose-(1-4)-2,3-di-O-methyl-beta-D-glucopyranuronic acid-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-3-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2,3,6-tri-O-sulfo-alpha-D-glucopyranoside / heparin pentasaccharide


Type: oligosaccharide, Oligosaccharide / Class: Anticoagulant / Mass: 1661.413 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: heparin pentasaccharide
DescriptorTypeProgram
WURCS=2.0/5,5,4/[a2122h-1a_1-5_1*OC_2*OSO/3=O/3=O_3*OSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O_3*OC][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122A-1b_1-5_2*OC_3*OC][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OC_4*OC_6*OSO/3=O/3=O]/1-2-3-4-5/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Glcp2SO33SO36SO3]{[(4+1)][a-L-IdopA2SO33Me]{[(4+1)][a-D-Glcp2SO33SO36SO3]{[(4+1)][b-D-GlcpA2Me3Me]{[(4+1)][a-D-Glcp2SO33Me4Me6SO3]{}}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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
Compound detailsHUMAN ANTITHROMBIN IS A PLASMA GLYCOPROTEIN, WITH 432 AMINO ACID RESIDUES AND FOUR GLYCOSYLATION ...HUMAN ANTITHROMBIN IS A PLASMA GLYCOPROTEIN, WITH 432 AMINO ACID RESIDUES AND FOUR GLYCOSYLATION SITES: ASN 96, ASN 135, ASN 155 AND ASN 192. THERE ARE TWO ANTITHROMBIN MOLECULES IN THE ASYMMETRIC UNIT: I AND L, BOTH ARE COMPLEXED BY THE HEPARIN PENTASACCHARIDE. FOR I MOLECULE, RESIDUES 1, 26-38, AND 432 WERE NOT BUILT BECAUSE OF POOR ELECTRON DENSITY MAPS. FOR L MOLECULE, RESIDUES 1-4, 26-38 AND 432 WERE NOT BUILT. THREE NAG MOLECULES, ATTACHED TO ASN 155 OF I MOLECULE, AND ASN 155 AND ASN 192 OF L MOLECULE, RESPECTIVELY, WERE BUILT INTO CLEAR DENSITY.

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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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 18-20 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlanithrombin11
212.2 mg/mlL-anithrombin11
34 mg/mlpentasaccharide11
430 %(w/v)PEG400011
50.05 %11NaN3
60.1 Msodium cacodylate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 60010 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 5.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
AMoREphasing
TNT5Drefinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→30 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 851 4 %RANDOM
Rwork0.195 ---
obs0.203 24096 94.2 %-
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6639 0 242 0 6881
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.005
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg1

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