[English] 日本語
Yorodumi
- PDB-7neu: Inhibitor Complex with Thrombin Activatable Fibrinolysis Inhibito... -

+
Open data


ID or keywords:

Loading...

-
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 / metallocarboxypeptidase activity / negative regulation of fibrinolysis / Metabolism of Angiotensinogen to Angiotensins / fibrinolysis / Regulation of Complement cascade / liver regeneration ...carboxypeptidase U / positive regulation of extracellular matrix constituent secretion / negative regulation of hepatocyte proliferation / negative regulation of plasminogen activation / metallocarboxypeptidase activity / negative regulation of fibrinolysis / Metabolism of Angiotensinogen to Angiotensins / fibrinolysis / Regulation of Complement cascade / liver regeneration / 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 / Zn_pept / Peptidase family M14 domain profile. / 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
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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


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

-
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


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


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


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

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more