[English] 日本語
Yorodumi
- PDB-6yzk: Carborane closo-pentyl-sulfonamide in complex with CA IX mimic -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yzk
TitleCarborane closo-pentyl-sulfonamide in complex with CA IX mimic
ComponentsCarbonic anhydrase 2
KeywordsLYASE / CARBONIC ANHYDRASE / CA INHIBITOR
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase
Similarity search - Domain/homology
Carborane closo-pentyl-sulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.99 Å
AuthorsKugler, M. / Brynda, J. / Pospisilova, K. / Rezacova, P.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Czech Science FoundationGA15-05677S Czech Republic
Other governmentTE01020028 Czech Republic
CitationJournal: J Enzyme Inhib Med Chem / Year: 2020
Title: The structural basis for the selectivity of sulfonamido dicarbaboranes toward cancer-associated carbonic anhydrase IX.
Authors: Kugler, M. / Holub, J. / Brynda, J. / Pospisilova, K. / Anwar, S.E. / Bavol, D. / Havranek, M. / Kral, V. / Fabry, M. / Gruner, B. / Rezacova, P.
History
DepositionMay 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5493
Polymers29,2011
Non-polymers3482
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.843, 41.249, 72.366
Angle α, β, γ (deg.)90.000, 103.960, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29200.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-Q3N / Carborane closo-pentyl-sulfonamide


Mass: 282.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12B10NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 sodium citrate, 50 mM Tris-H2SO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.99→35.11 Å / Num. obs: 116159 / % possible obs: 87 % / Redundancy: 3.544 % / Biso Wilson estimate: 12.988 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Rrim(I) all: 0.038 / Χ2: 1.062 / Net I/σ(I): 17.22 / Num. measured all: 411670
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
0.99-1.052.4710.4541.582595321546105020.7470.56348.7
1.05-1.123.3340.2473.715767920143173000.9290.29285.9
1.12-1.213.7340.1516.946617318834177240.9770.17694.1
1.21-1.333.670.10110.366062317348165170.9890.11895.2
1.33-1.483.8930.06816.285890315717151310.9950.07996.3
1.48-1.713.6120.04524.74841413862134020.9970.05396.7
1.71-2.13.7450.03236.234319311788115320.9990.03797.8
2.1-2.963.550.02742.9931824914689650.9990.03298
2.96-35.113.7180.02248.0618908515150860.9990.02698.7

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6GXE

6gxe


Resolution: 0.99→35.11 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.65 / SU ML: 0.015 / SU R Cruickshank DPI: 0.0215 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.022
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1426 2101 1.8 %RANDOM
Rwork0.1239 ---
obs0.1242 114058 87.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 59.68 Å2 / Biso mean: 14.058 Å2 / Biso min: 6.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å2-0.13 Å2
2--0.21 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: final / Resolution: 0.99→35.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 43 370 2435
Biso mean--15.98 26.1 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192292
X-RAY DIFFRACTIONr_bond_other_d0.0080.022110
X-RAY DIFFRACTIONr_angle_refined_deg1.6572.0363317
X-RAY DIFFRACTIONr_angle_other_deg5.27934969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9225296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82224.851101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.46215364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.832157
X-RAY DIFFRACTIONr_chiral_restr0.1070.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212559
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02508
X-RAY DIFFRACTIONr_rigid_bond_restr11.82332266
X-RAY DIFFRACTIONr_sphericity_free23.456536
X-RAY DIFFRACTIONr_sphericity_bonded9.05352429
LS refinement shellResolution: 0.99→1.015 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.254 70 -
Rwork0.263 3800 -
obs--39.35 %

+
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