[English] 日本語
Yorodumi
- PDB-9f2n: Structure of human carbonic anhydrase XII complexed with 3-(cyclo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9f2n
TitleStructure of human carbonic anhydrase XII complexed with 3-(cyclooctylamino)-2,6-difluoro-4-((3-hydroxypropyl)sulfonyl)-5-(piperidin-1-yl)benzenesulfonamide
ComponentsCarbonic anhydrase 12
KeywordsLYASE / DRUG DESIGN / CARBONIC ANHYDRASE / BENZENESULFONAMIDE
Function / homology
Function and homology information


chloride ion homeostasis / estrous cycle / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / basolateral plasma membrane / apical plasma membrane / zinc ion binding / membrane / plasma membrane
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
: / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsManakova, E.N. / Grazulis, S. / Paketuryte, V. / Smirnov, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
iNEXT-Discovery871037European Union
CitationJournal: To Be Published
Title: Structure of human carbonic anhydrase XII complexed with 3-(cyclooctylamino)-2,6-difluoro-4-((3-hydroxypropyl)sulfonyl)-5-(piperidin-1-yl)benzenesulfonamide
Authors: Manakova, E.N. / Grazulis, S. / Paketuryte, V. / Smirnov, A.
History
DepositionApr 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,32311
Polymers59,8352
Non-polymers1,4889
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint13 kcal/mol
Surface area21600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.093, 74.358, 75.846
Angle α, β, γ (deg.)90.00, 107.01, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Carbonic anhydrase 12 / Carbonate dehydratase XII / Carbonic anhydrase XII / CA-XII / Tumor antigen HOM-RCC-3.1.3


Mass: 29917.318 Da / Num. of mol.: 2 / Fragment: Human Carbonic anhydrase II
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Plasmid: pET31A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43570, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-A1H9A / 3-(cyclooctylamino)-2,6-difluoro-4-((3-hydroxypropyl)sulfonyl)-5-(piperidin-1-yl)benzenesulfonamide / 3-(cyclooctylamino)-2,6-bis(fluoranyl)-4-(3-oxidanylpropylsulfonyl)-5-piperidin-1-yl-benzenesulfonamide


Mass: 523.657 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H35F2N3O5S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Ammonium Citrate pH 7.0 0.1M; Ammonium Sulfate 0.2M; PEG4000 26%
PH range: 7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.905 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 1.21→72.53 Å / Num. obs: 147538 / % possible obs: 97.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.442 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Χ2: 1.04 / Net I/av σ(I): 2.6 / Net I/σ(I): 8.4
Reflection shellResolution: 1.21→1.23 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3726 / CC1/2: 0.602 / R split: 0.7 / Rpim(I) all: 0.72 / Χ2: 1.17 / % possible all: 50.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSVERSION Jan 10, 2022 BUILT=20220220data reduction
Aimless0.7.4data scaling
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→38.21 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.085 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18166 14636 9.9 %RANDOM
Rwork0.14322 ---
obs0.14706 132667 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.809 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å2-0.25 Å2
2--0.77 Å20 Å2
3---0.72 Å2
Refinement stepCycle: 1 / Resolution: 1.21→38.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4161 0 90 475 4726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124420
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.851.666026
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2535528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59523.547234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9915675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0711516
X-RAY DIFFRACTIONr_chiral_restr0.120.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023470
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.422.2182092
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.2863.3252614
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.4542.692328
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.27432.8276873
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.78334420
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.21→1.242 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 708 -
Rwork0.437 6146 -
obs--61.28 %

+
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