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- PDB-7neu: Inhibitor Complex with Thrombin Activatable Fibrinolysis Inhibito... -

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Basic information

Entry
Database: PDB / ID: 7neu
TitleInhibitor Complex with Thrombin Activatable Fibrinolysis Inhibitor (TAFIa)
ComponentsCarboxypeptidase B2
KeywordsHYDROLASE / Inhibitor / complex
Function / homology
Function and homology information


carboxypeptidase U / positive regulation of extracellular matrix constituent secretion / negative regulation of hepatocyte proliferation / negative regulation of plasminogen activation / Metabolism of Angiotensinogen to Angiotensins / negative regulation of fibrinolysis / metallocarboxypeptidase activity / fibrinolysis / liver regeneration / Regulation of Complement cascade ...carboxypeptidase U / positive regulation of extracellular matrix constituent secretion / negative regulation of hepatocyte proliferation / negative regulation of plasminogen activation / Metabolism of Angiotensinogen to Angiotensins / negative regulation of fibrinolysis / metallocarboxypeptidase activity / fibrinolysis / liver regeneration / Regulation of Complement cascade / cellular response to glucose stimulus / protein catabolic process / blood coagulation / response to xenobiotic stimulus / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region
Similarity search - Function
Carboxypeptidase B2 / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase
Similarity search - Domain/homology
Chem-U9K / Carboxypeptidase B2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsBrown, D.G. / Schaffner, A.P. / Vuillard, L.M. / Gloanec, P. / Raimbauld, E.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Phosphinanes and Azaphosphinanes as Potent and Selective Inhibitors of Activated Thrombin-Activatable Fibrinolysis Inhibitor (TAFIa).
Authors: Schaffner, A.P. / Sansilvestri-Morel, P. / Despaux, N. / Ruano, E. / Persigand, T. / Rupin, A. / Mennecier, P. / Vallez, M.O. / Raimbaud, E. / Desos, P. / Gloanec, P.
History
DepositionFeb 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxypeptidase B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0328
Polymers45,9631
Non-polymers1,0697
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-6 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.420, 157.350, 64.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Carboxypeptidase B2 / / Carboxypeptidase U / CPU / Plasma carboxypeptidase B / pCPB / Thrombin-activable fibrinolysis inhibitor / TAFI


Mass: 45963.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPB2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q96IY4, carboxypeptidase U
#7: 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.: 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 , 6 types, 34 molecules

#2: Chemical ChemComp-U9K / (1R,3S)-3-(4-ammoniobutyl)-1-(4-fluoro-2-(1-methyl-1H-imidazol-5-yl)benzyl)-1,4-azaphosphinan-1-ium-3-carboxylate 4,4-dioxide / 4-[(1~{R},3~{S})-3-carboxy-1-[[4-fluoranyl-2-(3-methylimidazol-4-yl)phenyl]methyl]-4-oxidanyl-4-oxidanylidene-1,4$l^{5}-azaphosphinan-1-ium-3-yl]butylazanium


Mass: 440.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30FN4O4P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.25 / Details: 100mM MES, 300mM Ammonium Chloride, 35% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.8→42.06 Å / Num. obs: 12711 / % possible obs: 99.4 % / Redundancy: 4.1 % / CC1/2: 0.01 / Rmerge(I) obs: 0.129 / Net I/σ(I): 14.48
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3.32 / Num. unique obs: 1240 / CC1/2: 0.001

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→42.02 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.821 / SU B: 38.84 / SU ML: 0.352 / Cross valid method: FREE R-VALUE / ESU R Free: 0.419
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2817 622 4.897 %
Rwork0.2012 12080 -
all0.205 --
obs-12702 99.359 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.706 Å2
Baniso -1Baniso -2Baniso -3
1--1.589 Å20 Å20 Å2
2--2.402 Å2-0 Å2
3----0.812 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3187 0 65 29 3281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133345
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173029
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.6514556
X-RAY DIFFRACTIONr_angle_other_deg1.2511.5836958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9815398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.07222.139173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69615519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4671518
X-RAY DIFFRACTIONr_chiral_restr0.0730.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023776
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02813
X-RAY DIFFRACTIONr_nbd_refined0.2130.2674
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22948
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21589
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21604
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.040.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1430.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.5680.24
X-RAY DIFFRACTIONr_nbd_other0.1440.222
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2710.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4520.21
X-RAY DIFFRACTIONr_mcbond_it0.5581.4361592
X-RAY DIFFRACTIONr_mcbond_other0.5581.4371591
X-RAY DIFFRACTIONr_mcangle_it1.0012.1521987
X-RAY DIFFRACTIONr_mcangle_other1.0012.1521988
X-RAY DIFFRACTIONr_scbond_it0.4751.4861753
X-RAY DIFFRACTIONr_scbond_other0.4751.4871754
X-RAY DIFFRACTIONr_scangle_it0.8722.2132568
X-RAY DIFFRACTIONr_scangle_other0.8722.2142569
X-RAY DIFFRACTIONr_lrange_it1.90916.1263727
X-RAY DIFFRACTIONr_lrange_other1.90316.1273727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8720.383500.329873X-RAY DIFFRACTION99.2473
2.872-2.9510.351550.304857X-RAY DIFFRACTION99.8905
2.951-3.0370.363470.275832X-RAY DIFFRACTION99.8864
3.037-3.130.374480.253797X-RAY DIFFRACTION99.5289
3.13-3.2320.401460.237787X-RAY DIFFRACTION99.4033
3.232-3.3460.258330.235761X-RAY DIFFRACTION99.0025
3.346-3.4720.278370.214722X-RAY DIFFRACTION99.6063
3.472-3.6130.228320.202719X-RAY DIFFRACTION99.6021
3.613-3.7740.255340.192698X-RAY DIFFRACTION99.7275
3.774-3.9570.23310.167646X-RAY DIFFRACTION99.4126
3.957-4.1710.255290.162628X-RAY DIFFRACTION99.5455
4.171-4.4230.256340.147577X-RAY DIFFRACTION99.3496
4.423-4.7280.177200.155578X-RAY DIFFRACTION100
4.728-5.1050.225240.149520X-RAY DIFFRACTION99.0893
5.105-5.590.261290.172479X-RAY DIFFRACTION99.6078
5.59-6.2470.234210.167452X-RAY DIFFRACTION99.789
6.247-7.2060.235200.17388X-RAY DIFFRACTION98.7893
7.206-8.810.225100.157343X-RAY DIFFRACTION99.7175
8.81-12.3910.225150.165266X-RAY DIFFRACTION98.5965
12.391-42.020.51370.325157X-RAY DIFFRACTION90.6077
Refinement TLS params.Method: refined / Origin x: -27.3585 Å / Origin y: -20.5237 Å / Origin z: 8.1501 Å
111213212223313233
T0.2166 Å20.0082 Å2-0.0191 Å2-0.0059 Å2-0.0119 Å2--0.1805 Å2
L0.8795 °20.1469 °2-0.5579 °2-1.0365 °2-0.2846 °2--1.9879 °2
S0.0109 Å °0.019 Å °-0.0238 Å °0.0317 Å °0.0035 Å °0.0113 Å °-0.0319 Å °-0.0961 Å °-0.0145 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 401
2X-RAY DIFFRACTION1ALLA501
3X-RAY DIFFRACTION1ALLA502

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