[English] 日本語
Yorodumi
- PDB-7sv2: Human Cytochrome P450 (CYP) 3A5 ternary complex with azamulin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7sv2
TitleHuman Cytochrome P450 (CYP) 3A5 ternary complex with azamulin
ComponentsCytochrome P450 3A5
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Inhibitor / complex / binding properties / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


retinoic acid 4-hydroxylase activity / estrogen 16-alpha-hydroxylase activity / lipid hydroxylation / aflatoxin metabolic process / testosterone 6-beta-hydroxylase activity / alkaloid catabolic process / Aflatoxin activation and detoxification / estrogen 2-hydroxylase activity / oxidative demethylation / Xenobiotics ...retinoic acid 4-hydroxylase activity / estrogen 16-alpha-hydroxylase activity / lipid hydroxylation / aflatoxin metabolic process / testosterone 6-beta-hydroxylase activity / alkaloid catabolic process / Aflatoxin activation and detoxification / estrogen 2-hydroxylase activity / oxidative demethylation / Xenobiotics / retinoic acid metabolic process / retinol metabolic process / estrogen metabolic process / unspecific monooxygenase / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / monooxygenase activity / oxygen binding / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane
Similarity search - Function
Cytochrome P450, E-class, group II / Cytochrome P450, E-class, CYP3A / : / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-MWY / Cytochrome P450 3A5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsHsu, M. / Johnson, E.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM031001 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural characterization of the homotropic cooperative binding of azamulin to human cytochrome P450 3A5.
Authors: Hsu, M.H. / Johnson, E.F.
History
DepositionNov 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450 3A5
B: Cytochrome P450 3A5
C: Cytochrome P450 3A5
D: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,74516
Polymers219,4504
Non-polymers6,29512
Water2,306128
1
A: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4364
Polymers54,8631
Non-polymers1,5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4364
Polymers54,8631
Non-polymers1,5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4364
Polymers54,8631
Non-polymers1,5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4364
Polymers54,8631
Non-polymers1,5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.786, 134.300, 275.274
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein
Cytochrome P450 3A5 / CYPIIIA5 / Cytochrome P450 HLp2 / Cytochrome P450-PCN3


Mass: 54862.586 Da / Num. of mol.: 4 / Fragment: UNP 24-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP3A5 / Plasmid: PCWORI / Production host: Escherichia coli (E. coli) / Strain (production host): DH-5A / References: UniProt: P20815, unspecific monooxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MWY / (3aS,4R,5S,6R,8R,9R,9aR,10R)-6-ethyl-5-hydroxy-4,6,9,10-tetramethyl-1-oxodecahydro-3a,9-propanocyclopenta[8]annulen-8-yl [(5-amino-1H-1,2,4-triazol-3-yl)sulfanyl]acetate


Mass: 478.648 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H38N4O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: Na Malonate, pH 6.5, 30% PEG 3350, n-decyl-beta-D-maltoside

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→39.56 Å / Num. obs: 85964 / % possible obs: 99.6 % / Redundancy: 12.1 % / Biso Wilson estimate: 50.98 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
2.46-2.5142410.5991
2.3-2.3442910.2021

-
Processing

Software
NameVersionClassification
JBluIce-EPICS1.19.2_4158data collection
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6mjm

6mjm


Resolution: 2.46→39.44 Å / SU ML: 0.2865 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8963
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2233 3400 4.81 %
Rwork0.1877 67252 -
obs0.1894 70652 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.54 Å2
Refinement stepCycle: LAST / Resolution: 2.46→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14651 0 436 128 15215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002815490
X-RAY DIFFRACTIONf_angle_d0.620521087
X-RAY DIFFRACTIONf_chiral_restr0.04382362
X-RAY DIFFRACTIONf_plane_restr0.0042670
X-RAY DIFFRACTIONf_dihedral_angle_d12.2226012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.50.30741470.25122804X-RAY DIFFRACTION99.97
2.5-2.530.32141310.25012752X-RAY DIFFRACTION100
2.53-2.570.31981360.25552829X-RAY DIFFRACTION100
2.57-2.610.30741360.24442718X-RAY DIFFRACTION99.89
2.61-2.660.32791390.23652796X-RAY DIFFRACTION99.93
2.66-2.710.29511430.23742752X-RAY DIFFRACTION100
2.71-2.760.29421410.23392814X-RAY DIFFRACTION100
2.76-2.820.26351200.21812775X-RAY DIFFRACTION100
2.82-2.880.28991370.22492762X-RAY DIFFRACTION99.93
2.88-2.940.2591290.23692844X-RAY DIFFRACTION99.9
2.94-3.020.28421320.22682751X-RAY DIFFRACTION100
3.02-3.10.26861550.21622778X-RAY DIFFRACTION99.97
3.1-3.190.26691440.20042778X-RAY DIFFRACTION99.97
3.19-3.290.21471410.20072815X-RAY DIFFRACTION100
3.29-3.410.26211650.21382772X-RAY DIFFRACTION99.93
3.41-3.550.25561580.20312784X-RAY DIFFRACTION99.9
3.55-3.710.21741550.19072782X-RAY DIFFRACTION99.97
3.71-3.90.18881390.16882789X-RAY DIFFRACTION99.83
3.9-4.150.20851470.16812796X-RAY DIFFRACTION99.76
4.15-4.470.19811400.16212839X-RAY DIFFRACTION99.87
4.47-4.920.17451370.15882805X-RAY DIFFRACTION99.73
4.92-5.630.20771600.17022848X-RAY DIFFRACTION99.97
5.63-7.080.20351410.18112872X-RAY DIFFRACTION99.9
7.08-39.440.16511270.15352997X-RAY DIFFRACTION99.81
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)
11.341840995340.3250809892930.372850446941.06005176359-0.1475574433061.26933562689-0.04554668190850.04915512774170.0435093355607-0.01374824896350.05476786984260.04881122798570.0191598379988-0.0414184655748-1.41785444417E-50.331241367251-0.05572239635830.01181825405650.262551894811-0.01261888703760.278868854398-11.95115351835.812200451740.2431705528
21.40968431157-0.322504961083-0.3808442197550.6897092048570.169360698370.946868676391-0.00387895854044-0.1930602179510.07456147287370.247077365293-0.0318624213845-0.187043106379-0.04909932021720.189600376152-0.003388006335470.420231537326-0.0905572585628-0.1853853824780.3694475927760.03806015176250.3418055203527.71648631867.470700405158.747547303
32.50329301845-0.5949501745870.1721635280171.3586417621-0.1413116099121.08782921703-0.0535457379064-0.02069078711670.1849336201730.0715561561480.03536866622790.0791893924266-0.122680764231-0.1089415102754.60391527489E-50.3189216574310.014493039969-0.02797031332820.2717120355890.009084774804820.24436714653138.578825348511.548042473722.7839466938
40.730560781282-0.1629482554380.2785259350370.9649129255020.1508920912291.19518243143-0.02295905888150.103542047309-0.0263401054367-0.1036742819280.0375993732859-0.3415076952510.1344635908580.201616316126.98213360332E-50.3037407290540.008501220955380.03263411520810.3551221477570.06519080912120.46191798530534.588354977650.524054605716.4973302083
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 23 through 495)AA23 - 4951 - 465
22(chain 'B' and resid 23 through 496)BE23 - 4961 - 465
33(chain 'C' and resid 29 through 496)CI29 - 4961 - 456
44(chain 'D' and resid 27 through 495)DM27 - 4951 - 438

+
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