[English] 日本語
Yorodumi
- PDB-6t0l: Crystal structure of CYP124 in complex with inhibitor compound 5' -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t0l
TitleCrystal structure of CYP124 in complex with inhibitor compound 5'
ComponentsCYP124 in complex with inhibitor compound 5'
KeywordsOXIDOREDUCTASE / Cytochrome / P450 / CYP / CYP124 / 124 / inhibition / inhibitor / drug / antituberculosis / tuberculosis / mycobacterium tuberculosis / compound / 5'
Function / homology
Function and homology information


methyl-branched lipid omega-hydroxylase / methyl-branched fatty acid metabolic process / cholesterol 26-hydroxylase activity / cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / fatty acid omega-oxidation / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / NADPH binding / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-M8N / DI(HYDROXYETHYL)ETHER / Methyl-branched lipid omega-hydroxylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBukhdruker, S. / Marin, E. / Varaksa, T. / Gilep, A. / Strushkevich, N. / Borshchevskiy, V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-54-00030 Russian Federation
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Metabolic Fate of Human Immunoactive Sterols in Mycobacterium tuberculosis.
Authors: Varaksa, T. / Bukhdruker, S. / Grabovec, I. / Marin, E. / Kavaleuski, A. / Gusach, A. / Kovalev, K. / Maslov, I. / Luginina, A. / Zabelskii, D. / Astashkin, R. / Shevtsov, M. / Smolskaya, S. ...Authors: Varaksa, T. / Bukhdruker, S. / Grabovec, I. / Marin, E. / Kavaleuski, A. / Gusach, A. / Kovalev, K. / Maslov, I. / Luginina, A. / Zabelskii, D. / Astashkin, R. / Shevtsov, M. / Smolskaya, S. / Kavaleuskaya, A. / Shabunya, P. / Baranovsky, A. / Dolgopalets, V. / Charnou, Y. / Savachka, A. / Litvinovskaya, R. / Hurski, A. / Shevchenko, E. / Rogachev, A. / Mishin, A. / Gordeliy, V. / Gabrielian, A. / Hurt, D.E. / Nikonenko, B. / Majorov, K. / Apt, A. / Rosenthal, A. / Gilep, A. / Borshchevskiy, V. / Strushkevich, N.
History
DepositionOct 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 3, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 2.0Feb 17, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / pdbx_nonpoly_scheme / struct_site_gen
Item: _atom_site.auth_seq_id / _citation.year ..._atom_site.auth_seq_id / _citation.year / _pdbx_nonpoly_scheme.pdb_seq_num / _struct_site_gen.auth_seq_id
Revision 2.1Jan 24, 2024Group: 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: CYP124 in complex with inhibitor compound 5'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3308
Polymers48,8691
Non-polymers1,4617
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-23 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.570, 71.570, 195.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein CYP124 in complex with inhibitor compound 5'


Mass: 48868.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P9WPP3

-
Non-polymers , 7 types, 387 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-M8N / ~{N}-[[[2-methyl-4-(3-methylbutyl)phenyl]amino]methyl]hydroxylamine


Mass: 222.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H22N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 3350, 0.1 M Bis-Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.66→30 Å / Num. obs: 60287 / % possible obs: 98.7 % / Redundancy: 11.7 % / Biso Wilson estimate: 28.85 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.12 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
7.42-301248.67990.9990.04497.7
5.25-7.4211.24113570.9980.05399.9
4.29-5.2512.145.117070.9990.05100
3.71-4.2912.943.119800.9990.052100
3.32-3.7112.936.922290.9990.06100
3.03-3.3211.728.524440.9990.079100
2.81-3.0312.623.426300.9980.107100
2.62-2.8113.118.328210.9970.142100
2.47-2.6213.51529760.9960.183100
2.35-2.4713.712.231650.9940.232100
2.24-2.3512.79.332850.9930.29999.9
2.14-2.2412.2734690.9860.393100
2.06-2.1413.15.435710.9760.533100
1.98-2.0613.33.937040.9870.698100
1.92-1.9813.12.838700.9390.937100
1.86-1.9212.7239870.8991.232100
1.8-1.8611.81.540810.8141.58799.9
1.75-1.89.60.941480.6612.14899.2
1.7-1.757.50.740910.5142.67594.3
1.66-1.76.20.539730.4013.55789.4

-
Processing

Software
NameVersionClassification
MxCuBE2data collection
XDS20190315data reduction
XSCALE20190315data scaling
PHASER2.8.3phasing
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T0F
Resolution: 1.8→29.67 Å / SU ML: 0.1722 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0601
RfactorNum. reflection% reflection
Rfree0.1923 2404 5 %
Rwork0.1633 --
obs0.1648 48050 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.58 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3327 0 94 380 3801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01093733
X-RAY DIFFRACTIONf_angle_d1.05455117
X-RAY DIFFRACTIONf_chiral_restr0.0602542
X-RAY DIFFRACTIONf_plane_restr0.0081682
X-RAY DIFFRACTIONf_dihedral_angle_d20.70051375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.30371400.28662640X-RAY DIFFRACTION99.71
1.84-1.880.3161370.27252602X-RAY DIFFRACTION99.38
1.88-1.920.26981400.24982623X-RAY DIFFRACTION99.82
1.92-1.970.30291390.2262644X-RAY DIFFRACTION99.78
1.97-2.020.23671390.2062639X-RAY DIFFRACTION99.61
2.02-2.080.20511380.18662636X-RAY DIFFRACTION99.82
2.08-2.150.22561390.1782644X-RAY DIFFRACTION99.89
2.15-2.220.21171390.17332665X-RAY DIFFRACTION99.93
2.22-2.310.21561400.17592665X-RAY DIFFRACTION99.82
2.31-2.420.2251400.16862656X-RAY DIFFRACTION99.89
2.42-2.550.20861410.16632680X-RAY DIFFRACTION99.93
2.55-2.710.21691400.15892674X-RAY DIFFRACTION100
2.71-2.920.17691430.1582699X-RAY DIFFRACTION100
2.92-3.210.18611430.16012716X-RAY DIFFRACTION100
3.21-3.670.19631430.14892733X-RAY DIFFRACTION100
3.67-4.620.14161470.12572784X-RAY DIFFRACTION100
4.62-29.670.16971560.16182946X-RAY DIFFRACTION99.94
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.69682929837-0.4519432775630.00022080616382.179712632770.3286856641192.369270902-0.1489319221670.1911530271230.118689396431-0.2192489105910.177482551788-0.236774050457-0.2589705153770.29642614022-0.018997845090.297352824886-0.0840991831580.003574363085710.293924555613-0.03041050299690.24469940826226.4945511962-0.39401990839247.4669922818
20.688601580874-0.00793026157012-0.03055262962580.9837106258150.4958243384761.57159477436-0.101931089587-0.01994528974350.01125996097840.06435818909230.136671823466-0.106107431293-0.1220208291980.298345571107-0.02480923887640.217707533937-0.0131525991571-0.02445795466460.216044585032-0.007987101315540.22589382555229.01106404773.6414317931266.0802880275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 428 )

+
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