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- PDB-5a1p: Crystal structure of cytochrome P450 3A4 bound to progesterone an... -

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Basic information

Entry
Database: PDB / ID: 5a1p
TitleCrystal structure of cytochrome P450 3A4 bound to progesterone and citrate
ComponentsCYTOCHROME P450 3A4
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 3A4 / CYP3A4 / MONOOXYGENASE / PROGESTERONE / CITRATE
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
CITRIC ACID / PROTOPORPHYRIN IX CONTAINING FE / PROGESTERONE / Cytochrome P450 3A4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSevrioukova, I. / Poulos, T.
CitationJournal: Biochemistry / Year: 2015
Title: Anion-Dependent Stimulation of Cyp3A4 Monooxygenase.
Authors: Sevrioukova, I.F. / Poulos, T.L.
History
DepositionMay 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME P450 3A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8814
Polymers55,7581
Non-polymers1,1233
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.340, 102.170, 125.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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 / 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 / Fragment: CATALYTIC DOMAIN, 23-503
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P08684, EC: 1.14.13.157, EC: 1.14.13.32, EC: 1.14.13.67, kynurenine 3-monooxygenase
#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-STR / PROGESTERONE


Mass: 314.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O2
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 3-22 DELETED, C-TERMINAL HIS-TAG 504-507

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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: 45.5 % / Description: NONE
Crystal growpH: 6.4
Details: 6% PEG 3350, 20 MM BIS-TRIS PROPANE PH 6.4, 12 MM AMMONIUM CITRATE, 5% GLYCEROL

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 2, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→65.85 Å / Num. obs: 16864 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 66.54 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.8 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TQN

1tqn


Resolution: 2.5→38.67 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 26.22 / Stereochemistry target values: ML
Details: RESIDUES 2, 23-25,265-267,282-285,AND 498-507 ARE DISORDERED AND NOT SEEN IN THE CRYSTAL STRUCTURE
RfactorNum. reflection% reflection
Rfree0.2779 858 5.1 %
Rwork0.1908 --
obs0.195 16850 95.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→38.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3738 0 79 7 3824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113946
X-RAY DIFFRACTIONf_angle_d1.615359
X-RAY DIFFRACTIONf_dihedral_angle_d16.6651508
X-RAY DIFFRACTIONf_chiral_restr0.058589
X-RAY DIFFRACTIONf_plane_restr0.008677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.65660.26221430.18262653X-RAY DIFFRACTION97
2.6566-2.86170.30791420.2152561X-RAY DIFFRACTION94
2.8617-3.14950.36451660.24292674X-RAY DIFFRACTION98
3.1495-3.6050.31291500.23072645X-RAY DIFFRACTION96
3.605-4.54080.26641380.17842710X-RAY DIFFRACTION97
4.5408-38.67460.23871190.16992749X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: -19.2533 Å / Origin y: 23.7077 Å / Origin z: 12.5368 Å
111213212223313233
T0.4435 Å20.0273 Å2-0.0029 Å2-0.4765 Å2-0.0659 Å2--0.3713 Å2
L3.511 °21.6141 °20.2909 °2-5.1738 °20.7475 °2--1.8467 °2
S0.0595 Å °-0.2986 Å °0.2833 Å °-0.1015 Å °-0.0946 Å °-0.2119 Å °-0.208 Å °-0.0649 Å °0.0262 Å °
Refinement TLS groupSelection details: (CHAIN A AND RESSEQ -10:9999)

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