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- PDB-1t1f: Crystal Structure of Native Antithrombin in its Monomeric Form -

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Basic information

Entry
Database: PDB / ID: 1t1f
TitleCrystal Structure of Native Antithrombin in its Monomeric Form
ComponentsAntithrombin-III
KeywordsBLOOD CLOTTING / serine-cysteine proteinase inhibitor / thrombin / human / x-ray crystallography
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 / protease binding / collagen-containing extracellular matrix ...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 / protease binding / collagen-containing extracellular matrix / blood microparticle / 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
IODIDE ION / Antithrombin-III
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsJohnson, D.J.D. / Huntington, J.A.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal structure of monomeric native antithrombin reveals a novel reactive center loop conformation
Authors: Johnson, D.J.D. / Langdown, J. / Li, W. / Luis, S.A. / Baglin, T.P. / Huntington, J.A.
History
DepositionApr 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)154,52036
Polymers147,2733
Non-polymers7,24733
Water3,891216
1
A: Antithrombin-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,50712
Polymers49,0911
Non-polymers2,41611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Antithrombin-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,50712
Polymers49,0911
Non-polymers2,41611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Antithrombin-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,50712
Polymers49,0911
Non-polymers2,41611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.830, 43.710, 153.930
Angle α, β, γ (deg.)90.00, 120.01, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Antithrombin-III / ATIII / PRO0309


Mass: 49091.066 Da / Num. of mol.: 3 / Mutation: S137A; V317C; T401C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: plasma / Gene: SERPINC1 / Organ: blood / Plasmid: pMASTOP / Cell (production host): Baby Hampster Kidney Cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01008

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Sugars , 2 types, 9 molecules

#2: 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.: 6
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
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 240 molecules

#4: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Sodium Iodide, PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 27, 2004
RadiationMonochromator: single crystal Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.75→38.52 Å / Num. all: 44339 / Num. obs: 44274 / % possible obs: 99.85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 72.038 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 5.6
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 1.7 / Num. unique all: 10553 / Rsym value: 0.512 / % possible all: 71.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1E04

1e04


Resolution: 2.75→38.46 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Used strict NCS throughout using matrices: ( -0.499 0.002 0.866 ) ( -0.003 1.000 -0.004 ) ( -0.866 -0.004 -0.499 ) with translation ( 76.83844 29.37406 133.27936 ) for the second monomer, ...Details: Used strict NCS throughout using matrices: ( -0.499 0.002 0.866 ) ( -0.003 1.000 -0.004 ) ( -0.866 -0.004 -0.499 ) with translation ( 76.83844 29.37406 133.27936 ) for the second monomer, and ( -0.49880 0.00217 -0.86671 ) ( -0.00089 1.00000 0.00302 ) ( 0.86672 0.00228 -0.49880 ) with translation ( 153.71411 14.59701 -0.03036 ) for the third monomer.
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 1796 4.1 %random
Rwork0.225 ---
all-44165 --
obs-44165 93.6 %-
Displacement parametersBiso mean: 59.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.497 Å20 Å2-0.534 Å2
2---14.006 Å20 Å2
3---9.509 Å2
Refinement stepCycle: LAST / Resolution: 2.75→38.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9756 0 324 216 10296
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.43
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_improper_angle_d0.88
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.373 217 -
Rwork0.373 --
obs-5532 71.5 %

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