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- PDB-7nee: Inhibitor Complex with Thrombin Activatable Fibrinolysis inhibito... -

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Basic information

Entry
Database: PDB / ID: 7nee
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-U9B / Carboxypeptidase B2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsBrown, D.G. / Schaffner, A.P. / Gloanec, P. / Raimbaud, E. / Vuillard, L.M.
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 3, 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
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxypeptidase B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3413
Polymers45,9331
Non-polymers4082
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.170, 95.500, 157.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 45932.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: S58063 / Source: (gene. exp.) Homo sapiens (human) / Gene: CPB2 / Production host: Homo sapiens (human) / References: UniProt: Q96IY4, carboxypeptidase U
#2: Chemical ChemComp-U9B / (1R,3S)-3-(4-ammoniobutyl)-1-benzyl-1,4-azaphosphinan-1-ium-3-carboxylate 4,4-dioxide / 4-[(1~{R},3~{S})-3-carboxy-4-oxidanyl-4-oxidanylidene-1-(phenylmethyl)-1,4$l^{5}-azaphosphinan-1-ium-3-yl]butylazanium


Mass: 342.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H27N2O4P / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 23% PEG 8000, 200mM Ammonium Citrate, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03324 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03324 Å / Relative weight: 1
ReflectionResolution: 2.55→37.384 Å / Num. obs: 15499 / % possible obs: 96.2 % / Redundancy: 3 % / Net I/σ(I): 9.5
Reflection shellResolution: 2.55→2.66 Å / Num. unique obs: 1862

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house model

Resolution: 2.55→37.384 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.861 / SU B: 40.539 / SU ML: 0.385 / Cross valid method: FREE R-VALUE / ESU R: 0.852 / ESU R Free: 0.387
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3156 773 5 %
Rwork0.2543 14686 -
all0.257 --
obs-15459 95.627 %
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: 39.852 Å2
Baniso -1Baniso -2Baniso -3
1-4.824 Å2-0 Å2-0 Å2
2---9.228 Å20 Å2
3---4.404 Å2
Refinement stepCycle: LAST / Resolution: 2.55→37.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3136 0 24 20 3180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133249
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172908
X-RAY DIFFRACTIONr_angle_refined_deg1.861.6334434
X-RAY DIFFRACTIONr_angle_other_deg1.2631.5696656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7555399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23322.407162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.00315481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5031515
X-RAY DIFFRACTIONr_chiral_restr0.0750.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023722
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02796
X-RAY DIFFRACTIONr_nbd_refined0.2230.2717
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.22885
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21506
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21551
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0940.23
X-RAY DIFFRACTIONr_metal_ion_refined0.2530.23
X-RAY DIFFRACTIONr_nbd_other0.1660.223
X-RAY DIFFRACTIONr_mcbond_it1.4812.5861599
X-RAY DIFFRACTIONr_mcbond_other1.4812.5861598
X-RAY DIFFRACTIONr_mcangle_it2.4923.8781997
X-RAY DIFFRACTIONr_mcangle_other2.4913.8781998
X-RAY DIFFRACTIONr_scbond_it1.3652.651650
X-RAY DIFFRACTIONr_scbond_other1.3612.6511649
X-RAY DIFFRACTIONr_scangle_it2.3333.9332437
X-RAY DIFFRACTIONr_scangle_other2.3323.9342438
X-RAY DIFFRACTIONr_lrange_it4.05329.3513623
X-RAY DIFFRACTIONr_lrange_other4.05329.353623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.6160.443640.3971081X-RAY DIFFRACTION94.3941
2.616-2.6880.376620.3761016X-RAY DIFFRACTION95.5674
2.688-2.7660.488460.3911026X-RAY DIFFRACTION96.4029
2.766-2.8510.492480.382986X-RAY DIFFRACTION97.1805
2.851-2.9450.467490.357984X-RAY DIFFRACTION96.9043
2.945-3.0480.42530.314937X-RAY DIFFRACTION96.5854
3.048-3.1630.375520.319901X-RAY DIFFRACTION96.8496
3.163-3.2920.377220.322874X-RAY DIFFRACTION95.8289
3.292-3.4380.365450.295827X-RAY DIFFRACTION95.719
3.438-3.6060.319440.266832X-RAY DIFFRACTION97.6589
3.606-3.8010.301320.223759X-RAY DIFFRACTION95.9951
3.801-4.0310.283440.206704X-RAY DIFFRACTION95.4082
4.031-4.310.269380.194670X-RAY DIFFRACTION94.9062
4.31-4.6550.29420.15618X-RAY DIFFRACTION95.5137
4.655-5.0980.178330.152586X-RAY DIFFRACTION95.2308
5.098-5.6990.203300.157529X-RAY DIFFRACTION94.7458
5.699-6.580.245240.201465X-RAY DIFFRACTION93.858
6.58-8.0550.314160.194406X-RAY DIFFRACTION92.1397
8.055-11.3760.227170.172312X-RAY DIFFRACTION93.7322
11.376-37.3840.233120.233173X-RAY DIFFRACTION85.6481
Refinement TLS params.Method: refined / Origin x: 7.8915 Å / Origin y: 20.8976 Å / Origin z: 18.699 Å
111213212223313233
T0.0084 Å2-0.0228 Å20.0021 Å2-0.5765 Å20.0017 Å2--0.0055 Å2
L0.4671 °2-0.0895 °2-0.0781 °2-0.0194 °20.0461 °2--0.5264 °2
S-0.0474 Å °0.017 Å °-0.0428 Å °0.0062 Å °0.0117 Å °0.01 Å °-0.0311 Å °0.0153 Å °0.0357 Å °
Refinement TLS groupSelection: ALL

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