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- PDB-5vcc: Crystal structure of human CYP3A4 bound to glycerol -

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Basic information

Entry
Database: PDB / ID: 5vcc
TitleCrystal structure of human CYP3A4 bound to glycerol
ComponentsCytochrome P450 3A4
KeywordsOXIDOREDUCTASE / cytochrome P450 / CYP3A4 / monooxygenase / glycerol
Function / homology
Function and homology information


quinine 3-monooxygenase / 1,8-cineole 2-exo-monooxygenase / albendazole monooxygenase (sulfoxide-forming) / quinine 3-monooxygenase activity / 1,8-cineole 2-exo-monooxygenase activity / 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity / vitamin D3 25-hydroxylase activity / vitamin D 24-hydroxylase activity / vitamin D catabolic process / retinoic acid 4-hydroxylase activity ...quinine 3-monooxygenase / 1,8-cineole 2-exo-monooxygenase / albendazole monooxygenase (sulfoxide-forming) / quinine 3-monooxygenase activity / 1,8-cineole 2-exo-monooxygenase activity / 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity / vitamin D3 25-hydroxylase activity / vitamin D 24-hydroxylase activity / vitamin D catabolic process / retinoic acid 4-hydroxylase activity / caffeine oxidase activity / estrogen 16-alpha-hydroxylase activity / lipid hydroxylation / aflatoxin metabolic process / anandamide 8,9 epoxidase activity / anandamide 11,12 epoxidase activity / anandamide 14,15 epoxidase activity / testosterone 6-beta-hydroxylase activity / alkaloid catabolic process / Aflatoxin activation and detoxification / Biosynthesis of maresin-like SPMs / monoterpenoid metabolic process / estrogen 2-hydroxylase activity / oxidative demethylation / vitamin D metabolic process / steroid catabolic process / Atorvastatin ADME / steroid hydroxylase activity / Xenobiotics / Phase I - Functionalization of compounds / retinoic acid metabolic process / retinol metabolic process / estrogen metabolic process / unspecific monooxygenase / long-chain fatty acid biosynthetic process / Prednisone ADME / Aspirin ADME / steroid metabolic process / androgen metabolic process / xenobiotic catabolic process / cholesterol metabolic process / steroid binding / xenobiotic metabolic process / monooxygenase activity / oxygen binding / lipid metabolic process / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / cytoplasm
Similarity search - Function
Cytochrome P450, E-class, group II / Cytochrome P450, E-class, CYP3A / : / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 ...Cytochrome P450, E-class, group II / Cytochrome P450, E-class, CYP3A / : / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 3A4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSevrioukova, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES025767 United States
CitationJournal: Biochemistry / Year: 2017
Title: High-Level Production and Properties of the Cysteine-Depleted Cytochrome P450 3A4.
Authors: Sevrioukova, I.F.
History
DepositionMar 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 3A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,85622
Polymers55,7581
Non-polymers2,09821
Water5,585310
1
A: Cytochrome P450 3A4
hetero molecules

A: Cytochrome P450 3A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,71244
Polymers111,5162
Non-polymers4,19642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
2
A: Cytochrome P450 3A4
hetero molecules

A: Cytochrome P450 3A4
hetero molecules

A: Cytochrome P450 3A4
hetero molecules

A: Cytochrome P450 3A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,42388
Polymers223,0314
Non-polymers8,39284
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area28540 Å2
ΔGint-20 kcal/mol
Surface area71200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.300, 98.910, 133.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-982-

HOH

21A-1008-

HOH

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Components

#1: Protein Cytochrome P450 3A4 / 1 / 8-cineole 2-exo-monooxygenase / Albendazole monooxygenase / Albendazole sulfoxidase / CYPIIIA3 ...1 / 8-cineole 2-exo-monooxygenase / Albendazole monooxygenase / Albendazole sulfoxidase / CYPIIIA3 / CYPIIIA4 / Cholesterol 25-hydroxylase / Cytochrome P450 3A3 / Cytochrome P450 HLp / Cytochrome P450 NF-25 / Cytochrome P450-PCN1 / Nifedipine oxidase / Quinine 3-monooxygenase / Taurochenodeoxycholate 6-alpha-hydroxylase


Mass: 55757.812 Da / Num. of mol.: 1
Mutation: 3-22 fragment deletion; C-terminal 4-histidine tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP3A4, CYP3A3 / Production host: Escherichia coli (E. coli)
References: UniProt: P08684, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen ...References: UniProt: P08684, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor, EC: 1.14.13.157, EC: 1.14.13.32, unspecific monooxygenase, EC: 1.14.13.67, EC: 1.14.13.97
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMA are the first two residues, fragment 3-22 deleted

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 298 K / Method: microbatch / Details: PEG4000

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.127 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.7→44.82 Å / Num. obs: 55451 / % possible obs: 99.3 % / Redundancy: 4.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.026 / Net I/σ(I): 12.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.951 / Mean I/σ(I) obs: 1.6 / Num. measured obs: 8108 / CC1/2: 0.514 / Rpim(I) all: 0.481 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TQN

1tqn


Resolution: 1.7→40.622 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.73
RfactorNum. reflection% reflection
Rfree0.2037 2811 5.07 %
Rwork0.1663 --
obs0.1682 55431 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→40.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3675 0 139 310 4124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074030
X-RAY DIFFRACTIONf_angle_d1.1145449
X-RAY DIFFRACTIONf_dihedral_angle_d13.6091559
X-RAY DIFFRACTIONf_chiral_restr0.045596
X-RAY DIFFRACTIONf_plane_restr0.006683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72930.27911290.29032641X-RAY DIFFRACTION100
1.7293-1.76080.3021490.26662608X-RAY DIFFRACTION100
1.7608-1.79460.32851520.24862609X-RAY DIFFRACTION100
1.7946-1.83130.26531360.23162628X-RAY DIFFRACTION100
1.8313-1.87110.26081140.22442632X-RAY DIFFRACTION100
1.8711-1.91460.24051490.20892622X-RAY DIFFRACTION100
1.9146-1.96250.241400.19342612X-RAY DIFFRACTION100
1.9625-2.01560.23851310.17562641X-RAY DIFFRACTION100
2.0156-2.07490.20271550.17072626X-RAY DIFFRACTION100
2.0749-2.14180.19891420.1662638X-RAY DIFFRACTION100
2.1418-2.21840.19251450.16472616X-RAY DIFFRACTION100
2.2184-2.30720.20371710.1632621X-RAY DIFFRACTION100
2.3072-2.41220.17141280.16032660X-RAY DIFFRACTION100
2.4122-2.53930.20251330.17162654X-RAY DIFFRACTION100
2.5393-2.69840.20991570.16712632X-RAY DIFFRACTION100
2.6984-2.90670.20651330.17262668X-RAY DIFFRACTION100
2.9067-3.19910.21921370.16662681X-RAY DIFFRACTION100
3.1991-3.66180.20031440.15772690X-RAY DIFFRACTION100
3.6618-4.61240.1791310.13622693X-RAY DIFFRACTION99
4.6124-40.6340.19571350.17342448X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: -19.1556 Å / Origin y: -26.1392 Å / Origin z: -14.7215 Å
111213212223313233
T0.232 Å2-0.002 Å2-0.0438 Å2-0.2814 Å20.0085 Å2--0.2242 Å2
L1.0511 °2-0.748 °20.3566 °2-2.5302 °2-0.5536 °2--1.0772 °2
S-0.1167 Å °-0.113 Å °0.0496 Å °0.3135 Å °0.0559 Å °0.1033 Å °-0.1991 Å °-0.1547 Å °0.0665 Å °
Refinement TLS groupSelection details: all

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