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- PDB-2ant: THE 2.6 A STRUCTURE OF ANTITHROMBIN INDICATES A CONFORMATIONAL CH... -

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Basic information

Entry
Database: PDB / ID: 2ant
TitleTHE 2.6 A STRUCTURE OF ANTITHROMBIN INDICATES A CONFORMATIONAL CHANGE AT THE HEPARIN BINDING SITE
ComponentsANTITHROMBIN
KeywordsSERPIN / HEPARIN / INHIBITOR
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 / : ...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 / : / 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
2-acetamido-2-deoxy-beta-D-allopyranose / Antithrombin-III
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSkinner, R. / Abrahams, J.-P. / Whisstock, J.C. / Lesk, A.M. / Carrell, R.W. / Wardell, M.R.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: The 2.6 A structure of antithrombin indicates a conformational change at the heparin binding site.
Authors: Skinner, R. / Abrahams, J.P. / Whisstock, J.C. / Lesk, A.M. / Carrell, R.W. / Wardell, M.R.
#1: Journal: To be Published
Title: Improved Diffraction of Antithrombin Crystals Grown in Microgravity
Authors: Wardell, M.R. / Skinner, R. / Carter, D.C. / Twigg, P.D. / Abrahams, J.-P.
History
DepositionJan 28, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: ANTITHROMBIN
I: ANTITHROMBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6444
Polymers98,2022
Non-polymers4422
Water1,42379
1
L: ANTITHROMBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3222
Polymers49,1011
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: ANTITHROMBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3222
Polymers49,1011
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.410, 98.310, 90.410
Angle α, β, γ (deg.)90.00, 103.32, 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: ANTITHROMBIN CRYSTALLISED AS A DIMER BETWEEN LATENT MOLECULE AND ONE ACTIVE MOLECULE
Source: (natural) Homo sapiens (human) / Tissue: PLASMA / References: UniProt: P01008
#2: Sugar ChemComp-NAA / 2-acetamido-2-deoxy-beta-D-allopyranose / N-acetyl-beta-D-allosamine / 2-acetamido-2-deoxy-beta-D-allose / 2-acetamido-2-deoxy-D-allose / 2-acetamido-2-deoxy-allose / N-ACETYL-D-ALLOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DAllpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-allosamineCOMMON NAMEGMML 1.0
b-D-AllpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AllNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 52.7 %
Crystal growpH: 6.7 / Details: 18% PEG 4000 50 MM NA/KPO4 PH 6.7
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 mMTris-HCl1drop
318-20 %(w/v)PEG40001reservoir
450 mMsodium potassium phosphate1reservoir
50.05 %(w/v)1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorDate: Apr 19, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 24646 / % possible obs: 74 % / Rmerge(I) obs: 0.048
Reflection shellResolution: 2.62→2.8 Å / % possible all: 53.9
Reflection
*PLUS
Redundancy: 1.8 %
Reflection shell
*PLUS
% possible obs: 53.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
TNT5Drefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ANT

1ant


Resolution: 2.6→26.9 Å / Cross valid method: RANDOM / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.29 682 3.3 %
Rwork0.217 --
all-24646 -
obs-24646 74 %
Refinement stepCycle: LAST / Resolution: 2.6→26.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6529 0 28 79 6636
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.09
X-RAY DIFFRACTIONt_angle_deg2.16
X-RAY DIFFRACTIONt_dihedral_angle_d20.053
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.05
X-RAY DIFFRACTIONt_gen_planes0.011
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.217 / Rfactor Rfree: 0.299
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.053
X-RAY DIFFRACTIONt_planar_d0.05
X-RAY DIFFRACTIONt_plane_restr0.011
LS refinement shell
*PLUS
Highest resolution: 2.64 Å / Lowest resolution: 2.72 Å / Rfactor Rfree: 0.63 / Rfactor obs: 0.37

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