[English] 日本語
Yorodumi
- PDB-6zr9: The crystal structure of the complex of hCAVII with 2-(4-benzhydr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zr9
TitleThe crystal structure of the complex of hCAVII with 2-(4-benzhydrylpiperazin-1-yl)-N-(4-sulfamoylphenyl)acetamide
ComponentsCarbonic anhydrase 7
KeywordsLYASE / CARBONIC ANHYDRASE VII / PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


positive regulation of cellular pH reduction / regulation of chloride transport / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / neuron cellular homeostasis / one-carbon metabolic process / zinc ion binding ...positive regulation of cellular pH reduction / regulation of chloride transport / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / neuron cellular homeostasis / one-carbon metabolic process / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Carbonic anhydrase VII / 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-QOZ / Carbonic anhydrase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsD'Ambrosio, K. / De Simone, G. / Di Fiore, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of EducationMOLIM ONCOBRAIN LAB Italy
CitationJournal: New J.Chem. / Year: 2021
Title: The crystal structures of 2-(4-benzhydrylpiperazin-1-yl)-N-(4-sulfamoylphenyl)acetamide in complex with human carbonic anhydrase II and VII provide insights into selective CA inhibitor development
Authors: D'Ambrosio, K. / Di Fiore, A. / Buonanno, M. / Kumari, S. / Tiwari, M. / Supuran, C.T. / Mishra, C.B. / Monti, S.M. / De Simone, G.
History
DepositionJul 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbonic anhydrase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4563
Polymers30,9261
Non-polymers5302
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.810, 88.600, 44.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Carbonic anhydrase 7 / / Carbonate dehydratase VII / Carbonic anhydrase VII / CA-VII


Mass: 30925.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA7 / Production host: Escherichia coli (E. coli) / References: UniProt: P43166, 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-QOZ / 2-[4-(diphenylmethyl)piperazin-1-yl]-~{N}-(4-sulfamoylphenyl)ethanamide


Mass: 464.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H28N4O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 3350, 0.2 M Ammonium acetate, 0.1 M Tris-HCl (pH 8.5)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU / Detector: CCD / Date: Nov 29, 2017 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 16529 / % possible obs: 95.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.029 / Rrim(I) all: 0.061 / Χ2: 1.035 / Net I/σ(I): 16.9 / Num. measured all: 61105
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.091.80.3757390.6830.330.5031.00188
2.09-2.121.90.3537380.7310.3110.4730.88985.8
2.12-2.161.90.3167530.7860.2780.4230.90688.5
2.16-2.2120.2587550.8320.2180.34190.1
2.21-2.262.20.2557720.8410.2050.3291.09291
2.26-2.312.40.2217730.9080.1690.281.02791.8
2.31-2.372.60.2078010.9230.1510.2581.09794
2.37-2.432.90.1957960.930.1340.2391.07495.3
2.43-2.53.20.1828290.9440.1180.2181.06597.4
2.5-2.583.30.1538480.9570.0960.1821.07998.1
2.58-2.683.50.1388400.9670.0850.1631.06498.5
2.68-2.783.70.118620.9830.0650.1291.0699.8
2.78-2.914.20.0958450.9870.0520.1090.996100
2.91-3.064.90.0838540.9930.0410.0931.024100
3.06-3.255.40.0648520.9960.030.071.024100
3.25-3.515.40.0478740.9980.0220.0521.093100
3.51-3.865.40.0418770.9990.0190.0450.999100
3.86-4.425.40.0318850.9990.0140.034199.9
4.42-5.565.30.0269030.9990.0120.0291.03699.7
5.56-5050.02493310.0110.0261.0497.1

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.05→33.4 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2411 938 5.5 %
Rwork0.196 14857 -
obs-15795 92.3 %
Solvent computationBsol: 50.3413 Å2
Displacement parametersBiso max: 64 Å2 / Biso mean: 25.2641 Å2 / Biso min: 7.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.626 Å20 Å20 Å2
2--1.227 Å20 Å2
3----0.601 Å2
Refinement stepCycle: final / Resolution: 2.05→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 34 103 2188
Biso mean--28.09 28.71 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.486
X-RAY DIFFRACTIONc_mcbond_it1.4011.5
X-RAY DIFFRACTIONc_scbond_it2.0322
X-RAY DIFFRACTIONc_mcangle_it2.2912
X-RAY DIFFRACTIONc_scangle_it2.9112.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.120.3805780.27491203128176.6
2.12-2.210.3089900.23441285137581.7
2.21-2.310.2908760.22591346142284.1
2.31-2.430.2782900.21491415150590.1
2.43-2.580.299960.22051511160795
2.58-2.780.24961110.21031564167597.8
2.78-3.060.2881920.21271572166498.6
3.06-3.50.2433930.19611621171499.5
3.5-4.410.18821030.16411639174299.7
4.41-33.40.18421090.16821701181098.7
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4ion_patch.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6ch19.param

+
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