[English] 日本語
Yorodumi
- PDB-6g5l: Crystal structure of human carbonic anhydrase isozyme XII with 4-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g5l
TitleCrystal structure of human carbonic anhydrase isozyme XII with 4-chloro-2-(cyclohexylamino)-N-(2-hydroxyethyl)-5-sulfamoyl-benzamide
ComponentsCarbonic anhydrase 12
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor comple
Function / homology
Function and homology information


chloride ion homeostasis / estrous cycle / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / basolateral plasma membrane / apical plasma membrane / zinc ion binding / membrane / plasma membrane
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-EM5 / DI(HYDROXYETHYL)ETHER / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.21 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Eur J Med Chem / Year: 2018
Title: Design of two-tail compounds with rotationally fixed benzenesulfonamide ring as inhibitors of carbonic anhydrases.
Authors: Zaksauskas, A. / Capkauskaite, E. / Jezepcikas, L. / Linkuviene, V. / Kisonaite, M. / Smirnov, A. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionMar 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)122,39126
Polymers119,6694
Non-polymers2,72222
Water18,6641036
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,19613
Polymers59,8352
Non-polymers1,36111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Carbonic anhydrase 12
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,19613
Polymers59,8352
Non-polymers1,36111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.127, 74.235, 91.527
Angle α, β, γ (deg.)90.000, 108.640, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains two dimers:

-
Components

-
Protein , 1 types, 4 molecules ABCD

#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.: 4 / Fragment: human carbonic anhydrase XII
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O43570, carbonic anhydrase

-
Non-polymers , 5 types, 1058 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Fragment: 4-chloro-2-(cyclohexylamino)-N-(2-hydroxyethyl)-5-sulfamoyl-benzamide
Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EM5 / 4-chloranyl-2-(cyclohexylamino)-~{N}-(2-hydroxyethyl)-5-sulfamoyl-benzamide


Mass: 375.871 Da / Num. of mol.: 4 / Fragment: Zn / Source method: obtained synthetically / Formula: C15H22ClN3O4S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Fragment: 1,2-ETHANEDIOL / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1036 / 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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: Crystallization buffer: 0.1M ammonium citrate (pH 7.2), 0.2 M ammonium sulfate and 30% PEG4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.975522 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975522 Å / Relative weight: 1
ReflectionResolution: 1.21→73.083 Å / Num. all: 284311 / Num. obs: 284311 / % possible obs: 95.9 % / Redundancy: 7 % / Rpim(I) all: 0.02 / Rrim(I) all: 0.053 / Rsym value: 0.043 / Net I/av σ(I): 4.278 / Net I/σ(I): 20.2 / Num. measured all: 1978101
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.21-1.286.60.50.4211.7266665401200.1910.50.4214.692.9
1.28-1.3570.3460.2922.5271141385670.1280.3460.2926.494.4
1.35-1.4570.2270.193.9255480364720.0850.2270.198.895.1
1.45-1.5670.1390.1136.5238944342350.0520.1390.11312.895.7
1.56-1.716.90.0890.0710.4217854316740.0340.0890.0718.196.1
1.71-1.917.10.060.04614.9204649288830.0220.060.04625.897
1.91-2.217.10.0440.03418.4184462258940.0160.0440.03436.298.3
2.21-2.7170.0390.0319.7153845218980.0150.0390.0342.498.4
2.71-3.8370.0380.03111.5120726171360.0140.0380.03149.999
3.83-73.0836.80.0490.048.66433594320.0190.0490.0452.698

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
Cootmodel building
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JD0

1jd0


Resolution: 1.21→73.08 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1804 / WRfactor Rwork: 0.1395 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8973 / SU R Cruickshank DPI: 0.0416 / SU Rfree: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1734 28370 10 %RANDOM
Rwork0.1359 255905 --
obs0.1396 284275 95.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 149.77 Å2 / Biso mean: 20.0494 Å2 / Biso min: 7.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å20.08 Å2
2--0.36 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.21→73.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8327 0 162 1036 9525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0198973
X-RAY DIFFRACTIONr_angle_refined_deg2.5141.96312232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96151082
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22824.69435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.059151366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3761529
X-RAY DIFFRACTIONr_chiral_restr0.1850.21273
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0217050
X-RAY DIFFRACTIONr_mcbond_it3.1231.6214280
X-RAY DIFFRACTIONr_mcangle_it3.6992.445378
X-RAY DIFFRACTIONr_scbond_it5.1231.9724693
X-RAY DIFFRACTIONr_rigid_bond_restr8.23538973
X-RAY DIFFRACTIONr_sphericity_free22.7945660
X-RAY DIFFRACTIONr_sphericity_bonded15.16359087
LS refinement shellResolution: 1.21→1.241 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 2093 -
Rwork0.176 18045 -
all-20138 -
obs--91.79 %

+
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