[English] 日本語
Yorodumi
- PDB-6b5a: Carbonic anhydrase IX-mimic in complex with nitrogenous base-bear... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b5a
TitleCarbonic anhydrase IX-mimic in complex with nitrogenous base-bearing benezenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE/INHIBITOR / carbonic anhydrase / inhibitor / benzenesulfonamide / purine / adenine / LYASE / LYASE-INHIBITOR complex
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 II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-CQS / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.622 Å
AuthorsLomelino, C.L. / McKenna, R.M.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: Discovery of New Sulfonamide Carbonic Anhydrase IX Inhibitors Incorporating Nitrogenous Bases.
Authors: Nocentini, A. / Bua, S. / Lomelino, C.L. / McKenna, R. / Menicatti, M. / Bartolucci, G. / Tenci, B. / Di Cesare Mannelli, L. / Ghelardini, C. / Gratteri, P. / Supuran, C.T.
History
DepositionSep 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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)29,2853
Polymers28,8441
Non-polymers4412
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11760 Å2
Unit cell
Length a, b, c (Å)42.015, 41.246, 71.766
Angle α, β, γ (deg.)90.000, 103.680, 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: 28844.465 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-CQS / 2-(6-amino-9H-purin-9-yl)-N-[2-(4-sulfamoylphenyl)ethyl]acetamide


Mass: 375.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N7O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6M NaCitrate 50mM Tris-HCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.62→29.014 Å / Num. obs: 31540 / % possible obs: 85.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 13.44 Å2 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.033 / Rrim(I) all: 0.058 / Χ2: 0.818 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.62-1.652.20.59113180.5590.4620.7540.78887.6
1.65-1.682.20.58513210.6920.4430.7370.81186.3
1.68-1.712.40.51513000.710.3940.6520.887.6
1.71-1.752.50.44313350.7680.3310.5560.78588.7
1.75-1.782.60.39113520.8150.2870.4880.77688.9
1.78-1.822.50.31113170.8710.230.3890.82988.2
1.82-1.872.50.26213270.8990.1980.330.78587.8
1.87-1.922.50.21613030.9390.1570.2690.77986.2
1.92-1.982.50.17312420.9480.1260.2150.88182.6
1.98-2.042.50.15312860.9640.1090.1890.81584.4
2.04-2.112.80.13112590.9790.0890.1590.88882.9
2.11-2.22.90.10611930.9840.0710.1280.83979.5
2.2-2.32.90.08412290.9870.0570.1020.79380.6
2.3-2.422.80.07312350.9890.050.0890.82381.3
2.42-2.572.60.05812250.9930.040.070.74680.1
2.57-2.772.80.04612010.9940.0310.0550.81679
2.77-3.0530.03511970.9960.0240.0420.76378.8
3.05-3.492.70.02712330.9970.0190.0330.79579.9
3.49-4.42.70.02314280.9970.0160.0280.91992.7
4.4-5030.02415710.9970.0160.0290.87798.2

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.622→29.014 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.63
RfactorNum. reflection% reflectionSelection details
Rfree0.2011 1583 5.02 %0.05
Rwork0.1549 ---
obs0.1573 31540 53.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.08 Å2 / Biso mean: 19.2481 Å2 / Biso min: 3.18 Å2
Refinement stepCycle: final / Resolution: 1.622→29.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 44 129 2215
Biso mean--29.39 20.52 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012146
X-RAY DIFFRACTIONf_angle_d1.1182921
X-RAY DIFFRACTIONf_chiral_restr0.06302
X-RAY DIFFRACTIONf_plane_restr0.009379
X-RAY DIFFRACTIONf_dihedral_angle_d14.0831257
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6221-1.67440.3595510.2591066111721
1.6744-1.73430.266690.21921360142927
1.7343-1.80370.2737870.20231656174332
1.8037-1.88580.21521140.18592047216140
1.8858-1.98520.2261390.16862378251747
1.9852-2.10950.23791350.16092813294855
2.1095-2.27230.19841610.15523202336362
2.2723-2.50090.2051890.14893446363568
2.5009-2.86250.20771970.16953679387672
2.8625-3.60530.24211920.15143642383471
3.6053-29.01910.15152490.13584668491791
Refinement TLS params.Method: refined / Origin x: -5.153 Å / Origin y: -1.6794 Å / Origin z: 85.6779 Å
111213212223313233
T-0.0734 Å20.0795 Å2-0.0407 Å2--0.1124 Å20.0177 Å2---0.0622 Å2
L0.0147 °2-0.0047 °20.0043 °2-0.0089 °2-0.0025 °2--0.0063 °2
S-0.0396 Å °-0.0054 Å °-0.0092 Å °-0.0393 Å °0.0593 Å °-0.0087 Å °-0.0153 Å °0.0088 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allD1 - 110
4X-RAY DIFFRACTION1allD111 - 118
5X-RAY DIFFRACTION1allD119 - 128
6X-RAY DIFFRACTION1allD129 - 133
7X-RAY DIFFRACTION1allC1

+
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