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- PDB-1br8: IMPLICATIONS FOR FUNCTION AND THERAPY OF A 2.9A STRUCTURE OF BINA... -

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Basic information

Entry
Database: PDB / ID: 1br8
TitleIMPLICATIONS FOR FUNCTION AND THERAPY OF A 2.9A STRUCTURE OF BINARY-COMPLEXED ANTITHROMBIN
Components
  • PROTEIN (ANTITHROMBIN-III)
  • PROTEIN (PEPTIDE)
KeywordsBLOOD CLOTTING / SERPINS / ANTITHROMBIN / BINARY-COMPLEX / HEPARIN / POLYMERISATION / THROMBOSIS / EMPHYSEMA / CIRRHOSIS
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSkinner, R. / Chang, W.S.W. / Jin, L. / Pei, X.Y. / Huntington, J.A. / Abrahams, J.P. / Carrell, R.W. / Lomas, D.A.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Implications for function and therapy of a 2.9 A structure of binary-complexed antithrombin.
Authors: Skinner, R. / Chang, W.S. / Jin, L. / Pei, X. / Huntington, J.A. / Abrahams, J.P. / Carrell, R.W. / Lomas, D.A.
History
DepositionAug 26, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 2, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 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
L: PROTEIN (ANTITHROMBIN-III)
I: PROTEIN (ANTITHROMBIN-III)
P: PROTEIN (PEPTIDE)


Theoretical massNumber of molelcules
Total (without water)99,2913
Polymers99,2913
Non-polymers00
Water41423
1
L: PROTEIN (ANTITHROMBIN-III)


Theoretical massNumber of molelcules
Total (without water)49,1011
Polymers49,1011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
I: PROTEIN (ANTITHROMBIN-III)
P: PROTEIN (PEPTIDE)


Theoretical massNumber of molelcules
Total (without water)50,1902
Polymers50,1902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-12 kcal/mol
Surface area17580 Å2
MethodPISA
3
L: PROTEIN (ANTITHROMBIN-III)

I: PROTEIN (ANTITHROMBIN-III)
P: PROTEIN (PEPTIDE)


Theoretical massNumber of molelcules
Total (without water)99,2913
Polymers99,2913
Non-polymers00
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation1_656x+1,y,z+11
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-18 kcal/mol
Surface area33750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.120, 101.690, 87.020
Angle α, β, γ (deg.)90.00, 104.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (ANTITHROMBIN-III)


Mass: 49101.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Strain: 1Q23-25 / Tissue: PLASMA / References: UniProt: P01008
#2: Protein/peptide PROTEIN (PEPTIDE)


Mass: 1089.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PEPTIDE WAS CHEMICALLY SYNTHESIZED.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.6 Å3/Da / Density % sol: 45 % / Description: DATA WERE COLLECTED USING OSCILLATION METHOD
Crystal growpH: 6.9
Details: 30.6% W/V PEG4000, 35% V/V GLYCEROL, 30 MM CACODYLATE, PH 6.9
Crystal
*PLUS
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
230.6 %(w/v)PEG400011
335 %(v/v)glycerol11
430 mMcacodylate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 23603 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 35.934 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 13.6
Reflection shellResolution: 2.94→3.12 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5.6 / % possible all: 87.8
Reflection shell
*PLUS
% possible obs: 87.8 % / Rmerge(I) obs: 0.13

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
AMoREphasing
TNT5refinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ANT

2ant


Resolution: 2.9→6 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.23 20419 -
obs-20419 87.8 %
Refinement stepCycle: LAST / Resolution: 2.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6503 0 0 23 6526
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.008663214
X-RAY DIFFRACTIONt_angle_deg1.02891625
X-RAY DIFFRACTIONt_dihedral_angle_d15.48399340
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0121772
X-RAY DIFFRACTIONt_gen_planes0.011937155
X-RAY DIFFRACTIONt_it3.376663215
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 6 Å / σ(F): 0 / Num. reflection Rfree: 898 / % reflection Rfree: 4.2 % / Rfactor all: 0.23 / Rfactor obs: 0.228 / Rfactor Rfree: 0.297 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_bond_d14
X-RAY DIFFRACTIONt_angle_deg251.02
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg4015.48
X-RAY DIFFRACTIONt_planar_d20.012
X-RAY DIFFRACTIONt_plane_restr1550.011

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