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- PDB-7mj5: complex of human thrombin with XC-43 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7mj5
Titlecomplex of human thrombin with XC-43
Components
  • Putative secreted salivary protein
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsBLOOD CLOTTING / inhibitor / serine protease / flea
Function / homology
Function and homology information


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 / regulation of blood coagulation / ligand-gated ion channel signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin ...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 / regulation of blood coagulation / ligand-gated ion channel signaling pathway / neutrophil-mediated killing of gram-negative bacterium / 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 / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / 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 / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / 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
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. ...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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Putative secreted salivary protein / Prothrombin
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopsylla cheopis (oriental rat flea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsLu, S. / Tirloni, L. / Andersen, J.F.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Identification of a substrate-like cleavage-resistant thrombin inhibitor from the saliva of the flea Xenopsylla cheopis.
Authors: Lu, S. / Tirloni, L. / Oliveira, M.B. / Bosio, C.F. / Nardone, G.A. / Zhang, Y. / Hinnebusch, B.J. / Ribeiro, J.M. / Andersen, J.F.
History
DepositionApr 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative secreted salivary protein
L: Thrombin light chain
H: Thrombin heavy chain
B: Thrombin light chain
C: Thrombin heavy chain
D: Thrombin light chain
E: Thrombin heavy chain
F: Thrombin light chain
G: Thrombin heavy chain
I: Thrombin light chain
J: Thrombin heavy chain
K: Thrombin light chain
M: Thrombin heavy chain
N: Putative secreted salivary protein
O: Putative secreted salivary protein
P: Putative secreted salivary protein
Q: Putative secreted salivary protein
R: Putative secreted salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,92930
Polymers226,46418
Non-polymers1,46512
Water20,9511163
1
A: Putative secreted salivary protein
L: Thrombin light chain
H: Thrombin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9885
Polymers37,7443
Non-polymers2442
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-36 kcal/mol
Surface area13610 Å2
MethodPISA
2
B: Thrombin light chain
C: Thrombin heavy chain
N: Putative secreted salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9885
Polymers37,7443
Non-polymers2442
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-35 kcal/mol
Surface area13760 Å2
MethodPISA
3
D: Thrombin light chain
E: Thrombin heavy chain
O: Putative secreted salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9885
Polymers37,7443
Non-polymers2442
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-33 kcal/mol
Surface area13360 Å2
MethodPISA
4
F: Thrombin light chain
G: Thrombin heavy chain
P: Putative secreted salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9885
Polymers37,7443
Non-polymers2442
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-35 kcal/mol
Surface area13430 Å2
MethodPISA
5
I: Thrombin light chain
J: Thrombin heavy chain
Q: Putative secreted salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9885
Polymers37,7443
Non-polymers2442
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-35 kcal/mol
Surface area13610 Å2
MethodPISA
6
K: Thrombin light chain
M: Thrombin heavy chain
R: Putative secreted salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9885
Polymers37,7443
Non-polymers2442
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-34 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.350, 136.320, 193.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 2 types, 12 molecules ANOPQRLBDFIK

#1: Protein/peptide
Putative secreted salivary protein


Mass: 3867.275 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Xenopsylla cheopis (oriental rat flea) / References: UniProt: A2IAB2
#2: Protein/peptide
Thrombin light chain / / Coagulation factor II


Mass: 4096.534 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin

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Protein / Sugars , 2 types, 12 molecules HCEGJM

#3: Protein
Thrombin heavy chain / / Coagulation factor II


Mass: 29780.219 Da / Num. of mol.: 6 / 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.: 6 / Source method: obtained synthetically / 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, 1169 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1163 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.32 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M magnesium acetate, 9 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→44.24 Å / Num. obs: 163186 / % possible obs: 99.9 % / Redundancy: 11.189 % / Biso Wilson estimate: 35.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.089 / Χ2: 0.925 / Net I/σ(I): 18.27 / Num. measured all: 1825903 / Scaling rejects: 374
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.2111.5980.6974.2213868311961119580.9420.729100
2.21-2.2711.470.5465.1813384811670116690.9630.572100
2.27-2.3311.2280.4446.1512724011337113320.9760.465100
2.33-2.410.480.3567.0811528311018110000.9780.37499.8
2.4-2.4811.0530.3038.3911843510717107150.9870.318100
2.48-2.5711.9670.26310.0312417010377103760.9910.275100
2.57-2.6711.9520.21212.02119078996399630.9930.221100
2.67-2.7811.7780.17214.38113712965696550.9940.18100
2.78-2.911.6610.14416.77107709923892370.9960.151100
2.9-3.0411.4440.12119.37101242884788470.9960.127100
3.04-3.2111.1220.09723.2193601841784160.9970.102100
3.21-3.410.5140.0826.2884078800579970.9980.08599.9
3.4-3.639.910.06729.8174249750474920.9980.0799.8
3.63-3.9311.3330.06135.3179601702470240.9980.064100
3.93-4.311.2150.05538.0472614647664750.9990.058100
4.3-4.8110.9370.05239.5464198587158700.9990.054100
4.81-5.5510.7230.0538.7356069522952290.9990.053100
5.55-6.89.780.04836.2443277444744250.9990.05199.5
6.8-9.6210.9070.04140.9938076349134910.9990.043100
9.62-44.2410.2930.03541.3620740202720150.9990.03699.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.97 Å58.41 Å
Translation2.97 Å58.41 Å

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PPB

1ppb


Resolution: 2.15→44.24 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 19.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1927 8012 5.04 %
Rwork0.1645 150851 -
obs0.1659 158863 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.47 Å2 / Biso mean: 43.0751 Å2 / Biso min: 22.6 Å2
Refinement stepCycle: final / Resolution: 2.15→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14984 0 90 1163 16237
Biso mean--72.36 43.59 -
Num. residues----1893
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.170.21932410.18144644488591
2.17-2.20.20572690.18084681495092
2.2-2.230.22832310.18224777500893
2.23-2.250.22092810.17734690497193
2.25-2.280.23112600.18014765502593
2.28-2.320.23652700.1774855512594
2.32-2.350.21942380.1774902514096
2.35-2.380.22912330.17654907514095
2.38-2.420.22762540.17534872512695
2.42-2.460.21052760.17174940521696
2.46-2.50.22252580.17284945520397
2.5-2.550.20912480.17974995524397
2.55-2.60.24152770.1925006528398
2.6-2.650.25552610.18695058531998
2.65-2.710.20622710.18595026529798
2.71-2.770.23923010.18165047534899
2.77-2.840.2092560.18025093534999
2.84-2.920.22792570.1885120537799
2.92-30.23642560.19145119537599
3-3.10.23072650.193951465411100
3.1-3.210.21572680.193151675435100
3.21-3.340.21982830.177251415424100
3.34-3.490.19742760.171251395415100
3.49-3.680.18142480.162452195467100
3.68-3.910.18452860.149551835469100
3.91-4.210.15493250.132951635488100
4.21-4.630.13592800.124452145494100
4.63-5.30.15942950.135252335528100
5.3-6.670.17542620.161553195581100
6.67-44.240.17752860.16954855771100
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)
12.64460.49280.76273.475-0.11542.4883-0.20520.25220.1511-0.39170.1285-0.3394-0.10080.3370.04250.3702-0.00210.08510.2632-0.00060.276829.568-31.82336.515
23.8192-0.2682-1.22571.5058-0.11421.7727-0.0039-0.22390.03950.1753-0.0123-0.1243-0.20820.12870.00060.4491-0.0041-0.10630.2693-0.03530.2524-25.465-51.01735.732
31.65130.6389-0.30266.9007-1.63052.81280.0682-0.1350.26380.16640.06150.268-0.2437-0.0755-0.13120.19660.01790.02870.3333-0.06520.26375.412-2.33327.183
43.5392-0.7590.53163.6423-0.44833.0979-0.1412-0.3089-0.21030.07840.06810.40510.1997-0.04790.0490.2498-0.02050.01750.36830.01950.3323-61.945-10.40257.022
53.76371.11930.49573.538-0.13053.2176-0.0202-0.2032-0.18750.46150.0604-0.219-0.10080.2992-0.02550.28720.070.01890.23750.08850.33977.404-15.56363.7
63.93510.59431.95342.45610.46663.26-0.0510.00470.30840.24940.01340.3096-0.1485-0.12790.12140.45310.08870.0850.28050.010.3805-8.5448.19356.826
71.2514-0.0140.49632.0297-0.22521.8234-0.0043-0.0959-0.11040.17250.07490.1892-0.032-0.151-0.06950.21450.01850.06930.26640.01650.2689-5.048-10.16257.852
84.631-0.75320.5475.3219-0.95557.10540.02660.08090.2466-0.0036-0.0342-0.451-0.18010.5850.03650.2413-0.08-0.050.3157-0.03330.3441-17.881-38.01566.999
91.6675-0.0540.08841.9422-0.05181.4451-0.0418-0.07110.0842-0.0049-0.03920.1541-0.0713-0.05360.08140.2518-0.0032-0.02960.2366-0.02370.2487-35.56-43.78565.756
106.0067-1.0122-0.87244.89540.8473.2766-0.3545-0.55310.00810.66040.1955-0.64780.13930.39020.12060.3320.0212-0.09990.38190.10780.430433.498-38.39964.991
111.5730.13390.03851.6025-0.10961.2452-0.04010.0013-0.2802-0.04790.0057-0.1960.06860.06360.04350.20960.00680.0250.2230.02650.39924.218-39.31748.626
126.36010.4733-0.9652.53350.05142.4094-0.03520.3112-0.6472-0.4141-0.0169-0.04190.31870.05840.04920.620.1254-0.05880.4492-0.07080.2756-31.746-69.59913.53
131.4013-0.2684-0.0071.10110.31931.13920.05620.19860.0193-0.2776-0.09650.0521-0.1902-0.05370.03840.43830.0859-0.06810.32650.00110.1907-35.086-54.33424.64
142.75870.5933-0.0145.7356-1.23893.8197-0.13630.254-0.1586-0.699-0.1572-0.69440.29120.4940.2480.5388-0.06830.16580.4547-0.0550.288924.469-13.3367.612
151.32840.2661-0.33692.002-0.34491.1359-0.09870.1939-0.0893-0.35910.08650.0470.1309-0.07390.01180.3708-0.0645-0.00380.3104-0.03670.18518.644-14.34217.996
163.3376-0.279-0.1735.4155-0.45452.8135-0.17130.2766-0.4631-0.5484-0.1156-0.41590.28270.27210.35360.41690.09020.14570.3478-0.0190.6331-53.894-17.41429.527
171.06270.0125-0.22971.9879-0.521.7324-0.0052-0.0406-0.12470.022-0.272-0.5464-0.0410.33720.23250.2048-0.01020.00040.33930.12250.553-52.846-6.93545.217
182.9328-0.64110.07054.5998-0.54664.09280.0401-0.3011-0.37320.2091-0.06420.36630.493-0.07120.08120.2052-0.05350.0870.240.00870.3359-39.639-57.66470.427
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN O AND RESID 6:35 )O6 - 35
2X-RAY DIFFRACTION2( CHAIN P AND RESID 6:34 )P6 - 34
3X-RAY DIFFRACTION3( CHAIN Q AND RESID 6:35 )Q6 - 35
4X-RAY DIFFRACTION4( CHAIN R AND RESID 6:35 )R6 - 35
5X-RAY DIFFRACTION5( CHAIN A AND RESID 5:35 )A5 - 35
6X-RAY DIFFRACTION6( CHAIN L AND RESID 6:22 )L6 - 22
7X-RAY DIFFRACTION7( CHAIN H AND ( RESID 16:245 OR RESID 301:301 ) )H16 - 245
8X-RAY DIFFRACTION7( CHAIN H AND ( RESID 16:245 OR RESID 301:301 ) )H301
9X-RAY DIFFRACTION8( CHAIN B AND RESID 5:22 )B5 - 22
10X-RAY DIFFRACTION9( CHAIN C AND ( RESID 16:246 OR RESID 301:301 ) )C16 - 246
11X-RAY DIFFRACTION9( CHAIN C AND ( RESID 16:246 OR RESID 301:301 ) )C301
12X-RAY DIFFRACTION10( CHAIN D AND RESID 7:22 )D7 - 22
13X-RAY DIFFRACTION11( CHAIN E AND RESID 16:245 )E16 - 245
14X-RAY DIFFRACTION12( CHAIN F AND RESID 7:22 )F7 - 22
15X-RAY DIFFRACTION13( CHAIN G AND ( RESID 16:246 OR RESID 301:301 ) )G16 - 246
16X-RAY DIFFRACTION13( CHAIN G AND ( RESID 16:246 OR RESID 301:301 ) )G301
17X-RAY DIFFRACTION14( CHAIN I AND RESID 5:23 )I5 - 23
18X-RAY DIFFRACTION15( CHAIN J AND ( RESID 16:246 OR RESID 301:301 ) )J16 - 246
19X-RAY DIFFRACTION15( CHAIN J AND ( RESID 16:246 OR RESID 301:301 ) )J301
20X-RAY DIFFRACTION16( CHAIN K AND RESID 7:23 )K7 - 23
21X-RAY DIFFRACTION17( CHAIN M AND RESID 16:247 )M16 - 247
22X-RAY DIFFRACTION18( CHAIN N AND RESID 6:35 )N6 - 35

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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