[English] 日本語
Yorodumi
- PDB-3okv: Human Carbonic Anhydrase II A65S, N67Q (CA IX mimic) bound with 2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3okv
TitleHuman Carbonic Anhydrase II A65S, N67Q (CA IX mimic) bound with 2-Ethylestrone 3-O-sulfamate
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Mixes alpha/beta fold / Reversible hydration of Carbon Dioxide to Bicarbonate
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 / morphogenesis of an epithelium ...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 / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 / 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-VZ4 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSippel, K.H. / Stander, B.A. / Robbins, A.H. / Tu, C.K. / Agbandje-McKenna, M. / Silverman, D.N. / Joubert, A.M. / McKenna, R.
Citation
Journal: LETT.DRUG DES.DISCOVERY / Year: 2011
Title: Characterization of Carbonic Anhydrase Isozyme Specific Inhibition by Sulfamated 2-Ethylestra Compounds
Authors: Sippel, K.H. / Stander, B.A. / Robbins, A.H. / Tu, C.K. / Agbandje-McKenna, M. / Silverman, D.N. / Joubert, A.M. / McKenna, R.
#1: Journal: Biochemistry / Year: 2010
Title: Structures of human carbonic anhydrase II/inhibitor complexes reveal a second binding site for steroidal and nonsteroidal inhibitors.
Authors: Cozier, G.E. / Leese, M.P. / Lloyd, M.D. / Baker, M.D. / Thiyagarajan, N. / Acharya, K.R. / Potter, B.V.
#2: Journal: Biochemistry / Year: 2009
Title: Design of a carbonic anhydrase IX active-site mimic to screen inhibitors for possible anticancer properties.
Authors: Genis, C. / Sippel, K.H. / Case, N. / Cao, W. / Avvaru, B.S. / Tartaglia, L.J. / Govindasamy, L. / Tu, C. / Agbandje-McKenna, M. / Silverman, D.N. / Rosser, C.J. / McKenna, R.
History
DepositionAug 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2185
Polymers29,3191
Non-polymers8994
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.263, 41.297, 72.397
Angle α, β, γ (deg.)90.00, 104.32, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 29319.086 Da / Num. of mol.: 1 / Mutation: A65S, N67Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / 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-VZ4 / (9beta)-2-ethyl-17-oxoestra-1(10),2,4-trien-3-yl sulfamate


Mass: 377.498 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H27NO4S
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 41.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.4 M Sodium citrate, 100mM Tris, 7.5 mM 2-Ethylestrone 3-O-sulfamate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 8, 2010 / Details: Osmic mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 40167 / Num. obs: 40167 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rsym value: 0.051 / Net I/σ(I): 28.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.45-1.54.50.1817.970.181176.9
1.5-1.565.80.14412.20.144192.9
1.56-1.635.70.11414.30.114193.4
1.63-1.725.70.09215.50.092194.2
1.72-1.835.70.07419.40.074194.8
1.83-1.975.80.05927.10.059196.6
1.97-2.176.10.05130.70.051197.3
2.17-2.486.20.04932.30.049198.2
2.48-3.126.20.04733.40.047199.1
3.12-505.70.04630.80.046196.6

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.3_467refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.6.3_467phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ili

2ili


Resolution: 1.45→28.704 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.15 / Isotropic thermal model: TLS / σ(F): 0 / Phase error: 13.18 / Stereochemistry target values: ML
Details: Individual coordinate and ADP refinement, rigid body, TLS, riding hydrogen, occupancy
RfactorNum. reflection% reflection
Rfree0.147 2005 5.01 %
Rwork0.1316 --
obs0.1323 39985 92.22 %
all-40167 -
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.33 Å2 / ksol: 0.455 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.07 Å2-0 Å20.1548 Å2
2---0.0194 Å20 Å2
3---1.0894 Å2
Refinement stepCycle: LAST / Resolution: 1.45→28.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 57 366 2474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092453
X-RAY DIFFRACTIONf_angle_d1.3833391
X-RAY DIFFRACTIONf_dihedral_angle_d13.309974
X-RAY DIFFRACTIONf_chiral_restr0.079357
X-RAY DIFFRACTIONf_plane_restr0.008442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48390.35291020.31441586X-RAY DIFFRACTION55
1.4839-1.5240.2571200.22512516X-RAY DIFFRACTION85
1.524-1.56880.18341470.17582686X-RAY DIFFRACTION92
1.5688-1.61950.16851380.13752693X-RAY DIFFRACTION93
1.6195-1.67740.15241390.12972760X-RAY DIFFRACTION93
1.6774-1.74450.14661520.12812751X-RAY DIFFRACTION94
1.7445-1.82390.16161390.12562775X-RAY DIFFRACTION95
1.8239-1.920.15471520.12212800X-RAY DIFFRACTION96
1.92-2.04030.14851560.12712847X-RAY DIFFRACTION97
2.0403-2.19780.14621530.12982887X-RAY DIFFRACTION98
2.1978-2.41880.13011480.11962886X-RAY DIFFRACTION98
2.4188-2.76860.14441560.12272926X-RAY DIFFRACTION99
2.7686-3.48720.13151510.12352963X-RAY DIFFRACTION99
3.4872-28.70930.12851520.12812904X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5855-0.3846-0.29620.37030.02290.0668-0.01650.0636-0.1752-0.0749-0.0752-0.2808-0.02240.09760.08880.1174-0.01920.05620.1833-0.00550.22856.6971-4.442911.5257
20.2325-0.26820.32360.6574-0.30750.6295-0.109-0.1824-0.00580.09470.0989-0.0789-0.0150.01390.00130.06740.01870.00090.118-0.00630.0603-4.154-2.526527.983
30.5125-0.03820.05160.09660.13540.33030.034-0.00420.1187-0.0769-0.0050.0561-0.1208-0.0375-0.01170.09820.00650.00050.06620.01870.1184-16.78137.297813.2276
40.4214-0.07720.00250.3705-0.07460.41580.00810.0057-0.0116-0.06730.00330.00190.00450.0081-0.0080.0708-0.0019-0.00180.06030.00620.0643-10.549-3.127613.6016
50.83360.0588-0.43170.5764-0.13880.2518-0.0609-0.22680.03310.12770.13990.04320.0528-0.0163-0.06940.08880.01940.0050.15790.00350.0657-11.1858-2.876834.6465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 4:9)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 10:45)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 46:87)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 88:251)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 252:261)

+
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