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- PDB-1dzg: N135Q-S380C-ANTITHROMBIN-III -

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Basic information

Entry
Database: PDB / ID: 1dzg
TitleN135Q-S380C-ANTITHROMBIN-III
Components(ANTITHROMBIN- ...) x 2
KeywordsBLOOD CLOTTING / SERPIN
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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMcCoy, A.J. / Huntington, J.A. / Carrell, R.W.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The Conformational Activation of Antithrombin. A 2. 85-A Structure of a Fluorescein Derivative Reveals an Electrostatic Link between the Hinge and Heparin Binding Regions.
Authors: Huntington, J.A. / Mccoy, A.J. / Belzar, K.J. / Pei, X.Y. / Gettins, P.G.W. / Carrell, R.W.
History
DepositionFeb 28, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2000Provider: repository / Type: Initial release
Revision 1.1May 26, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / 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.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: ANTITHROMBIN-III
L: ANTITHROMBIN-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,35310
Polymers98,2322
Non-polymers2,1218
Water724
1
L: ANTITHROMBIN-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2635
Polymers49,1011
Non-polymers1,1624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
I: ANTITHROMBIN-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0905
Polymers49,1311
Non-polymers9594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.610, 99.540, 88.690
Angle α, β, γ (deg.)90.00, 104.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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ANTITHROMBIN- ... , 2 types, 2 molecules IL

#1: Protein ANTITHROMBIN-III / / ATIII / SERPIN C1


Mass: 49131.105 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: INHIBITORY CONFORMATION / Source: (gene. exp.) HOMO SAPIENS (human)
Description: RECOMBINANT. BABY HAMSTER KIDNEY (BHK) CELL EXPRESSION
Plasmid: PMASTOP / Production host: CRICETIDAE SP. (mammal) / References: UniProt: P01008
#2: Protein ANTITHROMBIN-III / / ATIII / SERPIN C1


Mass: 49101.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PLASMA ALPHA ANTITHROMBIN-III / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P01008

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Sugars , 2 types, 6 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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.: 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

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Non-polymers , 2 types, 6 molecules

#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCHAIN I: HAS ENGINEERED MUTATIONS N135Q AND S380C N135Q MUTATION TO REMOVE GLYCOSYLATION SITE S380C ...CHAIN I: HAS ENGINEERED MUTATIONS N135Q AND S380C N135Q MUTATION TO REMOVE GLYCOSYLATION SITE S380C MUTATION FOR FLUORESCEIN ATTACHMENT SITE
Sequence detailsANT3_HUMAN RESIDUE NUMBERING IN SWS IS FROM START OF ANTITHROMBIN-III LEADER SEQUENCE. STRUCTURE ...ANT3_HUMAN RESIDUE NUMBERING IN SWS IS FROM START OF ANTITHROMBIN-III LEADER SEQUENCE. STRUCTURE RESIDUE NUMBERING IS FROM START OF MATURE ANTITHROMBIN-III RESIDUES NOT MODELLED HAD POOR ELECTRON 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: 3.17 Å3/Da / Density % sol: 62 %
Crystal growpH: 6.5
Details: 5MG/ML 1:1 MIX OF INHIBITORY: LATENT ANTITHROMBIN-III, 10.5% PEG 4000, 65 MM NACACODYLATE, PH 6.5
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein11
210.5 %PEG400011
365 mMsodium cacodylate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.88
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 98714 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 7.4
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 27983 / Num. measured all: 98714

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ANT

2ant


Resolution: 2.8→20 Å / SU B: 23.25 / SU ML: 0.4309 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 6.82723 / ESU R Free: 0.42762 / Details: BULK SOLVENT CORRECTION CALCULATED WITH CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1430 5 %SAME AS 2ANT
Rwork0.228 ---
obs-27983 98.3 %-
Displacement parametersBiso mean: 66 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6451 0 138 4 6593
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.01
X-RAY DIFFRACTIONp_angle_d0.0210.015
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.020.02
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.4733
X-RAY DIFFRACTIONp_mcangle_it4.3495
X-RAY DIFFRACTIONp_scbond_it3.6644
X-RAY DIFFRACTIONp_scangle_it5.8926
X-RAY DIFFRACTIONp_plane_restr0.0070.015
X-RAY DIFFRACTIONp_chiral_restr0.2010.15
X-RAY DIFFRACTIONp_singtor_nbd0.1530.15
X-RAY DIFFRACTIONp_multtor_nbd0.2030.15
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2050.15
X-RAY DIFFRACTIONp_xyhbond_nbd0.1270.15
X-RAY DIFFRACTIONp_planar_tor4.17
X-RAY DIFFRACTIONp_staggered_tor21.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_bond_d / Dev ideal: 0.011

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