[English] 日本語
Yorodumi
- PDB-7slx: Vanin-1 complexed with Compound 11 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7slx
TitleVanin-1 complexed with Compound 11
ComponentsPantetheinase
KeywordsHYDROLASE / Pantetheine / SBDD / pyrimdine carboxamide
Function / homology
Function and homology information


pantetheine hydrolase / pantetheine hydrolase activity / pantothenate metabolic process / chronic inflammatory response / coenzyme A catabolic process / Vitamin B5 (pantothenate) metabolism / Post-translational modification: synthesis of GPI-anchored proteins / positive regulation of T cell differentiation in thymus / acute inflammatory response / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway ...pantetheine hydrolase / pantetheine hydrolase activity / pantothenate metabolic process / chronic inflammatory response / coenzyme A catabolic process / Vitamin B5 (pantothenate) metabolism / Post-translational modification: synthesis of GPI-anchored proteins / positive regulation of T cell differentiation in thymus / acute inflammatory response / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / azurophil granule membrane / side of membrane / cell-cell adhesion / response to oxidative stress / inflammatory response / innate immune response / Neutrophil degranulation / extracellular region / membrane / plasma membrane
Similarity search - Function
Biotinidase-like, eukaryotic / Biotinidase/VNN family / Vanin, C-terminal / Vanin C-terminal domain / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
Chem-9SS / Pantetheinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsVajdos, F.F.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery of a Series of Pyrimidine Carboxamides as Inhibitors of Vanin-1.
Authors: Casimiro-Garcia, A. / Allais, C. / Brennan, A. / Choi, C. / Dower, G. / Farley, K.A. / Fleming, M. / Flick, A. / Frisbie, R.K. / Hall, J. / Hepworth, D. / Jones, H. / Knafels, J.D. / Kortum, ...Authors: Casimiro-Garcia, A. / Allais, C. / Brennan, A. / Choi, C. / Dower, G. / Farley, K.A. / Fleming, M. / Flick, A. / Frisbie, R.K. / Hall, J. / Hepworth, D. / Jones, H. / Knafels, J.D. / Kortum, S. / Lovering, F.E. / Mathias, J.P. / Mohan, S. / Morgan, P.M. / Parng, C. / Parris, K. / Pullen, N. / Schlerman, F. / Stansfield, J. / Strohbach, J.W. / Vajdos, F.F. / Vincent, F. / Wang, H. / Wang, X. / Webster, R. / Wright, S.W.
History
DepositionOct 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pantetheinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2927
Polymers53,8181
Non-polymers2,4746
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.550, 111.830, 147.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Pantetheinase / Pantetheine hydrolase / Tiff66 / Vascular non-inflammatory molecule 1 / Vanin-1


Mass: 53817.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VNN1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O95497, pantetheine hydrolase

-
Sugars , 3 types, 4 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D- ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DManpb1-6[DManpb1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / 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

-
Non-polymers , 3 types, 220 molecules

#5: Chemical ChemComp-9SS / (3R)-1-(2-{[1-(pyrimidin-5-yl)cyclopropyl]amino}pyrimidine-5-carbonyl)piperidine-3-carbonitrile


Mass: 349.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19N7O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES pH 6.1-6.7, 22-33% PEG-MME-2000, 10 mM TCEP
PH range: 6.1-6.7

-
Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→59.14 Å / Num. obs: 22429 / % possible obs: 98.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 64.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.021 / Rrim(I) all: 0.052 / Net I/σ(I): 22.8 / Num. measured all: 138910
Reflection shellResolution: 2.35→2.62 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.518 / Num. measured all: 39698 / Num. unique obs: 6246 / CC1/2: 0.921 / Rpim(I) all: 0.224 / Rrim(I) all: 0.566 / Net I/σ(I) obs: 3.4 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.1.29data scaling
BUSTER2.11.5refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→25.63 Å / Cor.coef. Fo:Fc: 0.9446 / Cor.coef. Fo:Fc free: 0.9231 / SU R Cruickshank DPI: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.354 / SU Rfree Blow DPI: 0.219 / SU Rfree Cruickshank DPI: 0.217
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 1112 4.99 %RANDOM
Rwork0.1739 ---
obs0.1761 22272 98.31 %-
Displacement parametersBiso max: 149.43 Å2 / Biso mean: 59.19 Å2 / Biso min: 30.11 Å2
Baniso -1Baniso -2Baniso -3
1-2.2193 Å20 Å20 Å2
2---15.5478 Å20 Å2
3---13.3286 Å2
Refine analyzeLuzzati coordinate error obs: 0.265 Å
Refinement stepCycle: final / Resolution: 2.35→25.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 166 218 4004
Biso mean--73.56 64.88 -
Num. residues----461
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1325SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes577HARMONIC5
X-RAY DIFFRACTIONt_it3919HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion543SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4501SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3919HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5380HARMONIC21.28
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion18.62
LS refinement shellResolution: 2.35→2.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2756 161 5.59 %
Rwork0.222 2719 -
all0.2251 2880 -
obs--98.31 %

+
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://pdbjlvh1.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