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- PDB-1r1l: Structure of dimeric antithrombin complexed with a P14-P9 reactiv... -

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Basic information

Entry
Database: PDB / ID: 1r1l
TitleStructure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide and an exogenous tripeptide (formyl-norleucine-LF)
Components
  • Antithrombin P14-P9 peptide
  • Antithrombin-III
  • EXOGENOUS TRIPEPTIDE formyl-(NLE)LF
KeywordsHYDROLASE/HYDROLASE INHIBITOR / serpin / loop-sheet polymer / beta-barrel / 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 / collagen-containing extracellular matrix / 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 / collagen-containing extracellular matrix / 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
FORMYL GROUP / Antithrombin-III
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhou, A. / Huntington, J.A. / Lomas, D.A. / Stein, P.E. / Carrell, R.W.
CitationJournal: To be Published
Title: Serpins and the design of peptides to block intermolecular beta-linkages
Authors: Zhou, A. / Huntington, J.A. / Lomas, D.A. / Stein, P.E. / Carrell, R.W.
History
DepositionSep 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 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 / 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 / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 23, 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 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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-(NLE)LF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,82513
Polymers99,1544
Non-polymers1,6719
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.171, 100.421, 87.198
Angle α, β, γ (deg.)90.00, 104.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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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 occurs naturally in Homo sapiens (human).
#3: Protein/peptide EXOGENOUS TRIPEPTIDE formyl-(NLE)LF


Mass: 391.505 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein / Sugars , 2 types, 9 molecules LI

#1: Protein Antithrombin-III / / ATIII / PRO0309


Mass: 49101.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood / References: UniProt: P01008
#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.: 7
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 , 3 types, 121 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FOR / FORMYL GROUP / Aldehyde


Mass: 30.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.42 %
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, temperature 298K

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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: Dec 4, 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: 2.7→25.08 Å / Num. all: 31741 / Num. obs: 31707 / % possible obs: 99.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 59.3 Å2 / Rmerge(I) obs: 0.163 / Rsym value: 0.135 / Net I/σ(I): 4.6
Reflection shellResolution: 2.7→2.87 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.053 / Mean I/σ(I) obs: 1.6 / Num. unique all: 5451 / Rsym value: 0.438 / % possible all: 99.5

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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: PDB ENTRY 1LK6

1lk6


Resolution: 2.7→24.99 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
Rfree0.249 1602 -Random
Rwork0.204 ---
obs-31687 99.5 %-
Displacement parametersBiso mean: 49 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å2-7.45 Å2
2--6.81 Å20 Å2
3----7.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.7→24.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6666 0 113 119 6898
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.36 264 -
Rwork0.312 --
obs-5013 99.9 %

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