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- PDB-5veu: Human Cytochrome P450 3A5 (CYP3A5) -

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Basic information

Entry
Database: PDB / ID: 5veu
TitleHuman Cytochrome P450 3A5 (CYP3A5)
ComponentsCytochrome P450 3A5
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / Inhibitor / Complex / Cytochrome P450 / ritonavir / CYP3A5 / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex
Function / homology
Function and homology information


testosterone 6-beta-hydroxylase activity / retinoic acid 4-hydroxylase activity / aflatoxin metabolic process / estrogen 16-alpha-hydroxylase activity / lipid hydroxylation / alkaloid catabolic process / Aflatoxin activation and detoxification / Xenobiotics / oxidative demethylation / estrogen metabolic process ...testosterone 6-beta-hydroxylase activity / retinoic acid 4-hydroxylase activity / aflatoxin metabolic process / estrogen 16-alpha-hydroxylase activity / lipid hydroxylation / alkaloid catabolic process / Aflatoxin activation and detoxification / Xenobiotics / oxidative demethylation / estrogen metabolic process / retinoic acid metabolic process / retinol metabolic process / unspecific monooxygenase / aromatase activity / 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 / 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
RITONAVIR / PROTOPORPHYRIN IX CONTAINING FE / RITONAVIR / Cytochrome P450 3A5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsHsu, M.-H. / 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: Mol. Pharmacol. / Year: 2018
Title: The X-Ray Crystal Structure of the Human Mono-Oxygenase Cytochrome P450 3A5-Ritonavir Complex Reveals Active Site Differences between P450s 3A4 and 3A5.
Authors: Hsu, M.H. / Savas, U. / Johnson, E.F.
History
DepositionApr 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 10, 2018Group: Structure summary / Category: pdbx_molecule_features
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 3A5
B: Cytochrome P450 3A5
C: Cytochrome P450 3A5
D: Cytochrome P450 3A5
E: Cytochrome P450 3A5
F: Cytochrome P450 3A5
G: Cytochrome P450 3A5
H: Cytochrome P450 3A5
I: Cytochrome P450 3A5
J: Cytochrome P450 3A5
K: Cytochrome P450 3A5
L: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)667,91227
Polymers658,35112
Non-polymers9,56115
Water0
1
A: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2003
Polymers54,8631
Non-polymers1,3372
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2003
Polymers54,8631
Non-polymers1,3372
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4792
Polymers54,8631
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4792
Polymers54,8631
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4792
Polymers54,8631
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4792
Polymers54,8631
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4792
Polymers54,8631
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2003
Polymers54,8631
Non-polymers1,3372
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4792
Polymers54,8631
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4792
Polymers54,8631
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4792
Polymers54,8631
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Cytochrome P450 3A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4792
Polymers54,8631
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.988, 198.384, 234.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 54862.586 Da / Num. of mol.: 12 / Fragment: UNP residues 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 / Heme B


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-RIT / RITONAVIR / / A-84538 / Ritonavir


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 720.944 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C37H48N6O5S2 / References: RITONAVIR / Comment: medication, antiretroviral*YM

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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: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, PEG 300, ADA, zinc sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.106965 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.106965 Å / Relative weight: 1
ReflectionResolution: 2.91→39.16 Å / Num. obs: 152197 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 70 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.023 / Net I/av σ(I): 2.8 / Net I/σ(I): 17
Reflection shellResolution: 2.91→2.96 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7276 / CC1/2: 0.848 / Rpim(I) all: 0.277 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NXU

3nxu


Resolution: 2.91→39.155 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.27 / Phase error: 26.98
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 7549 4.96 %Random Selection
Rwork0.2137 ---
obs0.2159 152082 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.91→39.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44074 0 666 0 44740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00545903
X-RAY DIFFRACTIONf_angle_d1.06662309
X-RAY DIFFRACTIONf_dihedral_angle_d11.7317549
X-RAY DIFFRACTIONf_chiral_restr0.0676945
X-RAY DIFFRACTIONf_plane_restr0.0057917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9097-2.94280.37812320.31034548X-RAY DIFFRACTION95
2.9428-2.97740.33252680.28854794X-RAY DIFFRACTION100
2.9774-3.01370.3482510.28414813X-RAY DIFFRACTION100
3.0137-3.05180.34332710.26864760X-RAY DIFFRACTION100
3.0518-3.09190.30622520.26634745X-RAY DIFFRACTION100
3.0919-3.13430.33322570.26984802X-RAY DIFFRACTION100
3.1343-3.1790.33442550.26424783X-RAY DIFFRACTION100
3.179-3.22650.33322600.26314765X-RAY DIFFRACTION100
3.2265-3.27690.31732500.26644765X-RAY DIFFRACTION100
3.2769-3.33060.30122680.26534771X-RAY DIFFRACTION100
3.3306-3.3880.3112540.25974814X-RAY DIFFRACTION100
3.388-3.44950.30912880.25164754X-RAY DIFFRACTION100
3.4495-3.51580.30822450.24554786X-RAY DIFFRACTION100
3.5158-3.58750.28972480.24414802X-RAY DIFFRACTION100
3.5875-3.66550.26832440.23614823X-RAY DIFFRACTION100
3.6655-3.75070.27152650.22944800X-RAY DIFFRACTION100
3.7507-3.84440.26722430.22234803X-RAY DIFFRACTION100
3.8444-3.94830.28012650.22154772X-RAY DIFFRACTION100
3.9483-4.06430.25572490.21814833X-RAY DIFFRACTION100
4.0643-4.19540.2312280.2054839X-RAY DIFFRACTION100
4.1954-4.34510.25492400.20224840X-RAY DIFFRACTION100
4.3451-4.51890.23482510.1934869X-RAY DIFFRACTION100
4.5189-4.72420.23962250.19894841X-RAY DIFFRACTION100
4.7242-4.97280.24392510.18934882X-RAY DIFFRACTION100
4.9728-5.28370.24272530.19354822X-RAY DIFFRACTION100
5.2837-5.69050.21222760.19814857X-RAY DIFFRACTION100
5.6905-6.26110.2452410.20724873X-RAY DIFFRACTION100
6.2611-7.16230.23462210.19884952X-RAY DIFFRACTION100
7.1623-9.00560.18442430.16424944X-RAY DIFFRACTION99
9.0056-39.15880.21132550.17345081X-RAY DIFFRACTION99

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