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- PDB-1lk6: Structure of dimeric antithrombin complexed with a P14-P9 reactiv... -

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Basic information

Entry
Database: PDB / ID: 1lk6
TitleStructure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide and an exogenous tripeptide
Components
  • antithrombin P14-P9 peptide
  • antithrombin-III
  • exogenous tripeptide formyl-MLF
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Loop-sheet polymer / beta-barrel / BLOOD CLOTTING / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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-alpha-D-glucopyranose / Antithrombin-III
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhou, A. / Huntington, J.A. / Lomas, D.A. / Carrell, R.W. / Stein, P.E.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Serpin Polymerization Is Prevented by a Hydrogen Bond Network That Is Centered on His-334 and Stabilized by Glycerol
Authors: Zhou, A. / Stein, P.E. / Huntington, J.A. / Carrell, R.W.
History
DepositionApr 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / 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_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 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
Revision 2.2Oct 16, 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: antithrombin-III
I: antithrombin-III
C: antithrombin P14-P9 peptide
D: exogenous tripeptide formyl-MLF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,06213
Polymers99,2004
Non-polymers1,8629
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-1 kcal/mol
Surface area34640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.811, 99.908, 87.292
Angle α, β, γ (deg.)90.00, 104.44, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules LI

#1: Protein antithrombin-III / serine (or cysteine) proteinase inhibitor / clade C / antithrombin / member 1 / antithrombin III


Mass: 49101.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood / Tissue fraction: plasma / References: UniProt: P01008

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Protein/peptide , 2 types, 2 molecules CD

#2: Protein/peptide antithrombin P14-P9 peptide


Mass: 560.556 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence ocurs naturally in human antithrombin
#3: Protein/peptide exogenous tripeptide formyl-MLF


Mass: 437.553 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Sugars , 2 types, 8 molecules

#4: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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, 35 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.07 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 4000, sodium cacodylate, ammonium fluoride, glycerol, pH 6.8, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
114 mg/mlprotein1drop
210-20 %PEG40001reservoir
350 mMsodium cacodylate1reservoirpH6.8
40.2 M1reservoirNH4F
512 %glycerol1reservoiror without

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 2002 / Details: mirrors
RadiationMonochromator: cooled liquid gallium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.8→37.58 Å / Num. all: 27398 / Num. obs: 27376 / % possible obs: 96.7 % / Observed criterion σ(I): -3.7 / Redundancy: 3.3 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.087 / Net I/σ(I): 7.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 1.7 / Num. unique all: 3351 / Rsym value: 0.431 / % possible all: 81.5
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. measured all: 91051
Reflection shell
*PLUS
Lowest resolution: 2.93 Å / % possible obs: 81.5 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
CNSrefinement
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Dimeric antithrombin complexed with a P14-P8 reactive loop peptide and an exogenous tetrapeptide (1jvq). Both peptides omitted in starting model

1jvq


Resolution: 2.8→34.03 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum likelihood target
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1374 5 %Random
Rwork0.202 ---
all-28306 --
obs-27351 96.6 %-
Displacement parametersBiso mean: 55.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å2-5.53 Å2
2--9.09 Å20 Å2
3----8.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.8→34.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6603 0 126 34 6763
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.8-2.930.3461500.3480.028281379.7
2.93-3.080.2871340.2890.025329293.8
3.08-3.270.2641640.2640.021354599.9
3.27-3.530.2271810.2260.0173502100
3.52-3.880.2141700.2130.016354499.9
3.88-4.440.1742170.1720.012351999.9
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 34 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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