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- PDB-4e05: Anophelin from the malaria vector inhibits thrombin through a nov... -

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Basic information

Entry
Database: PDB / ID: 400000
TitleAnophelin from the malaria vector inhibits thrombin through a novel reverse-binding mechanism
Components
  • (Thrombin) x 2
  • Salivary anti-thrombin peptide anophelin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


molecular function inhibitor activity / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway ...molecular function inhibitor activity / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cytosolic calcium ion concentration / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / Golgi lumen / positive regulation of protein localization to nucleus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Salivary thrombin inhibitor anophelin, mosquito / Thrombin inhibitor from mosquito / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily ...Salivary thrombin inhibitor anophelin, mosquito / Thrombin inhibitor from mosquito / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Prothrombin / Salivary anti-thrombin peptide anophelin
Similarity search - Component
Biological speciesAnopheles albimanus (mosquito)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.304 Å
AuthorsFigueiredo, A.C. / de Sanctis, D. / Gutierrez-Gallego, R. / Cereija, T.B. / Macedo-Ribeiro, S. / Fuentes-Prior, P. / Pereira, P.J.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Unique thrombin inhibition mechanism by anophelin, an anticoagulant from the malaria vector.
Authors: Figueiredo, A.C. / de Sanctis, D. / Gutierrez-Gallego, R. / Cereija, T.B. / Macedo-Ribeiro, S. / Fuentes-Prior, P. / Pereira, P.J.
History
DepositionMar 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Thrombin
H: Thrombin
I: Salivary anti-thrombin peptide anophelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6645
Polymers40,4193
Non-polymers2442
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-29 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.180, 120.180, 77.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11L-406-

HOH

21H-771-

HOH

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Components

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Protein , 2 types, 2 molecules HI

#2: Protein Thrombin / / Coagulation factor II


Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: heavy chain (UNP residues 364-622) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#3: Protein Salivary anti-thrombin peptide anophelin


Mass: 6542.695 Da / Num. of mol.: 1 / Fragment: mature anophelin (UNP residues 23-83)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles albimanus (mosquito) / Gene: anophelin / Plasmid: pTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q9NJS1

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Protein/peptide / Sugars , 2 types, 2 molecules L

#1: Protein/peptide Thrombin / / Coagulation factor II


Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: light chain (UNP residues 328-363) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#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.: 1
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, 88 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 1

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Sample preparation

CrystalDensity Matthews: 4.01 Å3/Da / Density % sol: 69.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 1.4 M tri-sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.304→104.079 Å / Num. all: 28423 / Num. obs: 28423 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rsym value: 0.061 / Net I/σ(I): 16.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.304-2.434.10.6831.11679741130.68399
2.43-2.585.90.3951.92301638830.395100
2.58-2.756.30.2383.22311436830.238100
2.75-2.976.30.1415.22160934410.141100
2.97-3.266.30.08481972231500.084100
3.26-3.646.20.05610.21784428670.056100
3.64-4.216.20.04611.91556125210.046100
4.21-5.156.10.04313.11311021490.043100
5.15-7.295.90.04213.6993116760.042100
7.29-62.325.70.03914.153459400.03998.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U69

3u69


Resolution: 2.304→32.658 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.78 / σ(F): 1.35 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 1438 5.06 %RANDOM
Rwork0.1693 ---
obs0.1709 28396 99.74 %-
all-28423 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.86 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso max: 193.35 Å2 / Biso mean: 63.1407 Å2 / Biso min: 32.99 Å2
Baniso -1Baniso -2Baniso -3
1--12.4073 Å20 Å20 Å2
2---12.4073 Å2-0 Å2
3---24.8146 Å2
Refinement stepCycle: LAST / Resolution: 2.304→32.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2509 0 15 87 2611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092591
X-RAY DIFFRACTIONf_angle_d1.0593497
X-RAY DIFFRACTIONf_chiral_restr0.073364
X-RAY DIFFRACTIONf_plane_restr0.004451
X-RAY DIFFRACTIONf_dihedral_angle_d14.093984
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.304-2.38660.34791450.31742651279699
2.3866-2.48210.33671460.298926552801100
2.4821-2.59510.30751410.256326972838100
2.5951-2.73180.24151570.215926822839100
2.7318-2.90290.2291500.186726722822100
2.9029-3.12680.19761380.185527072845100
3.1268-3.44120.22961570.174526782835100
3.4412-3.93840.18031370.148627112848100
3.9384-4.95920.14741280.124927452873100
4.9592-32.6610.17791390.15992760289999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1992-0.64411.05042.8546-0.50312.15890.13020.3886-0.0914-0.3377-0.1334-0.10910.04130.37580.02660.32770.00270.00970.39510.05120.369244.3012-1.20882.3464
22.401-0.90550.67343.1343-1.23172.08280.0754-0.0557-0.23440.03460.19290.7269-0.0183-0.2152-0.24840.2567-0.01130.00980.32180.09380.456131.4936-2.473310.5958
36.4717-2.609-2.63112.98233.09866.1860.07450.4884-0.8697-0.3273-0.08221.0130.4499-0.4990.1750.5355-0.0472-0.14160.35880.11390.544729.0802-7.86472.8042
46.52283.87875.51592.59343.18094.69930.7762-0.423-0.6516-0.75580.3431-2.88310.45692.7215-1.10240.78730.32040.24972.00960.00871.749162.4712-2.148-1.4531
51.8904-3.78611.41498.1606-1.87213.41360.10980.84921.7972-0.4177-0.1369-0.5567-0.1810.3157-0.02190.4108-0.0909-0.04240.39360.06360.463639.537211.60214.0227
69.64112.0365.83368.9161-0.06213.72820.4147-0.1825-1.30610.08750.39380.29560.68880.1156-0.93880.45120.0426-0.04720.4860.13670.737244.3496-16.601118.4342
75.80255.625-4.65375.4597-4.51363.7321.0354-0.91010.191.0431-0.48080.2343-0.38830.2584-0.66410.6182-0.04080.09320.5020.11870.670632.9571-8.578526.6877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain H and resid 321:408)H321 - 408
2X-RAY DIFFRACTION2(chain H and resid 409:552)H409 - 552
3X-RAY DIFFRACTION3(chain H and resid 553:579)H553 - 579
4X-RAY DIFFRACTION4(chain I and resid 32:39)I32 - 39
5X-RAY DIFFRACTION5(chain I and resid 40:61)I40 - 61
6X-RAY DIFFRACTION6(chain L and resid 290:305)L290 - 305
7X-RAY DIFFRACTION7(chain L and resid 306:318)L306 - 318

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