[English] 日本語
Yorodumi
- PDB-6uzu: Carbonic Anhydrase IX-mimic In Complex WITH U-CH3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uzu
TitleCarbonic Anhydrase IX-mimic In Complex WITH U-CH3
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / CAIX inhibitors / pH regulation / cancer therapeutics / transmembrane / LYASE-LYASE INHIBITOR complex / LYASE
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 / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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
Chem-6LU / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMcKenna, R. / Mboge, M.Y. / Mahon, B.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA165284-03S1 United States
CitationJournal: Eur J Med Chem / Year: 2017
Title: Structure activity study of carbonic anhydrase IX: Selective inhibition with ureido-substituted benzenesulfonamides.
Authors: Mboge, M.Y. / Mahon, B.P. / Lamas, N. / Socorro, L. / Carta, F. / Supuran, C.T. / Frost, S.C. / McKenna, R.
History
DepositionNov 15, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionOct 21, 2020ID: 5JN1
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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)29,3865
Polymers28,8441
Non-polymers5414
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.152, 41.364, 71.933
Angle α, β, γ (deg.)90.000, 103.830, 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 / Mutation: A65S, N67Q, E69T, I91L, F131V, K170E, L204A
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-6LU / 4-{[(3,5-dimethylphenyl)carbamoyl]amino}benzene-1-sulfonamide


Mass: 319.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N3O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.11 Å3/Da / Density % sol: 41.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6 M Na-Citrate, 50 mM Tris, pH 7.8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 65546 / % possible obs: 97.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.023 / Rrim(I) all: 0.063 / Χ2: 0.963 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.533.90.34715550.8710.1970.4010.80780.3
1.53-1.554.20.29316440.9080.1590.3350.83686.6
1.55-1.584.60.27217550.940.140.3080.82390.9
1.58-1.6250.24518280.9530.1190.2730.83895
1.62-1.655.90.23619020.9630.1040.2580.86998.8
1.65-1.696.90.23119450.9720.0930.2490.903100
1.69-1.737.20.18919350.9840.0740.2030.887100
1.73-1.787.40.15918940.9890.0620.1710.921100
1.78-1.837.50.13419410.9920.0520.1440.973100
1.83-1.897.50.11219530.9930.0440.120.98100
1.89-1.967.50.09119200.9950.0350.0980.976100
1.96-2.047.50.07719280.9960.030.0830.958100
2.04-2.137.50.06819480.9970.0260.0730.965100
2.13-2.247.50.05919410.9970.0230.0630.91100
2.24-2.387.50.05319260.9980.0210.0570.898100
2.38-2.567.50.04919650.9980.0190.0530.892100
2.56-2.827.50.04419380.9980.0170.0470.845100
2.82-3.237.50.03919640.9990.0150.0420.846100
3.23-4.077.50.03919600.9980.0150.0420.968100
4.07-507.20.04620320.9980.0180.0491.83699.6

-
Processing

Software
NameVersionClassification
PHENIX1.10pre_2097refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.5→29.094 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1842 3286 5.01 %
Rwork0.1611 62260 -
obs0.1623 65546 86.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.17 Å2 / Biso mean: 17.3568 Å2 / Biso min: 5.66 Å2
Refinement stepCycle: final / Resolution: 1.5→29.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 31 185 2258
Biso mean--18.89 26.27 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092137
X-RAY DIFFRACTIONf_angle_d1.3162902
X-RAY DIFFRACTIONf_chiral_restr0.069301
X-RAY DIFFRACTIONf_plane_restr0.013375
X-RAY DIFFRACTIONf_dihedral_angle_d10.5672176
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5001-1.52250.2680.2036127441
1.5225-1.54620.2306760.1841143346
1.5462-1.57160.1891840.1733159351
1.5716-1.59870.1528940.1528177157
1.5987-1.62780.18221070.158200365
1.6278-1.65910.17881120.1516235075
1.6591-1.69290.16721390.1509256482
1.6929-1.72970.1841590.1592279089
1.7297-1.770.19771490.1648291194
1.77-1.81420.171510.1689303798
1.8142-1.86330.1991540.1602310299
1.8633-1.91810.21081950.17163122100
1.9181-1.980.17561510.173142100
1.98-2.05070.22921590.15863107100
2.0507-2.13280.21581740.16333107100
2.1328-2.22990.22811570.16593137100
2.2299-2.34740.18521650.15493119100
2.3474-2.49440.17031620.16433127100
2.4944-2.68680.18911660.17473109100
2.6868-2.9570.19411670.17583166100
2.957-3.38430.17171660.16413060100
3.3843-4.26170.14651650.14093141100
4.2617-29.0940.17541660.1538309599
Refinement TLS params.Method: refined / Origin x: -5.4423 Å / Origin y: 1.2776 Å / Origin z: 85.7238 Å
111213212223313233
T0.0671 Å20.0027 Å20.002 Å2-0.0677 Å2-0.0028 Å2--0.067 Å2
L0.4825 °2-0.0191 °20.0728 °2-0.6076 °2-0.0399 °2--0.4127 °2
S-0.0002 Å °-0.0396 Å °0.0172 Å °-0.0511 Å °0.0067 Å °-0.0015 Å °-0.0062 Å °0.0171 Å °0.027 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allD1 - 197
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allE1 - 2

+
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