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- PDB-4m2t: Corrected Structure of Mouse P-glycoprotein bound to QZ59-SSS -

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Basic information

Entry
Database: PDB / ID: 4m2t
TitleCorrected Structure of Mouse P-glycoprotein bound to QZ59-SSS
ComponentsMultidrug resistance protein 1AMultiple drug resistance
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ATP-Binding Cassette Transporter / Multidrug Efflux / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


hormone transport / cellular response to borneol / response to codeine / response to cyclosporin A / Atorvastatin ADME / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug / response to quercetin / cellular response to external biotic stimulus ...hormone transport / cellular response to borneol / response to codeine / response to cyclosporin A / Atorvastatin ADME / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug / response to quercetin / cellular response to external biotic stimulus / regulation of intestinal absorption / response to antineoplastic agent / positive regulation of establishment of Sertoli cell barrier / Prednisone ADME / ceramide translocation / terpenoid transport / ceramide floppase activity / response to glycoside / carboxylic acid transmembrane transport / carboxylic acid transmembrane transporter activity / floppase activity / establishment of blood-retinal barrier / protein localization to bicellular tight junction / regulation of response to osmotic stress / ABC-family proteins mediated transport / cellular response to L-glutamate / response to thyroxine / establishment of blood-brain barrier / phosphatidylethanolamine flippase activity / xenobiotic transport across blood-brain barrier / phosphatidylcholine floppase activity / xenobiotic detoxification by transmembrane export across the plasma membrane / export across plasma membrane / intercellular canaliculus / ABC-type xenobiotic transporter / response to vitamin D / transepithelial transport / P-type phospholipid transporter / ABC-type xenobiotic transporter activity / response to vitamin A / response to glucagon / intestinal absorption / phospholipid translocation / cellular response to antibiotic / cellular hyperosmotic salinity response / maintenance of blood-brain barrier / cellular response to alkaloid / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / response to cadmium ion / lactation / cellular response to dexamethasone stimulus / regulation of chloride transport / stem cell proliferation / cellular response to estradiol stimulus / placenta development / brush border membrane / circadian rhythm / G2/M transition of mitotic cell cycle / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to hypoxia / response to xenobiotic stimulus / apical plasma membrane / ubiquitin protein ligase binding / cell surface / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-2J8 / ATP-dependent translocase ABCB1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.35 Å
AuthorsLi, J. / Jaimes, K.F. / Aller, S.G.
CitationJournal: Protein Sci. / Year: 2014
Title: Refined structures of mouse P-glycoprotein.
Authors: Li, J. / Jaimes, K.F. / Aller, S.G.
History
DepositionAug 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Multidrug resistance protein 1A
B: Multidrug resistance protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,1056
Polymers283,3552
Non-polymers2,7504
Water0
1
A: Multidrug resistance protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,0533
Polymers141,6781
Non-polymers1,3752
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Multidrug resistance protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,0533
Polymers141,6781
Non-polymers1,3752
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.742, 114.978, 375.810
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 Multidrug resistance protein 1A / Multiple drug resistance / ATP-binding cassette sub-family B member 1A / MDR1A / Multidrug resistance protein 3 / P-glycoprotein 3


Mass: 141677.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P21447, xenobiotic-transporting ATPase
#2: Chemical
ChemComp-2J8 / (4S,11S,18S)-4,11,18-tri(propan-2-yl)-6,13,20-triselena-3,10,17,22,23,24-hexaazatetracyclo[17.2.1.1~5,8~.1~12,15~]tetracosa-1(21),5(24),7,12(23),14,19(22)-hexaene-2,9,16-trione / cyclic-tris-(S)-valineselenazole / QZ59-SSS


Mass: 687.413 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H30N6O3Se3

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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: 3.73 Å3/Da / Density % sol: 66.99 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 4.35→20 Å / Num. all: 28400 / Num. obs: 28239 / % possible obs: 99.43 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 4.35→19.954 Å / SU ML: 0.61 / σ(F): 1.33 / Phase error: 32.12 / Stereochemistry target values: ML
Details: AUTHORS STATE THAT THIS STRUCTURE WAS REFINED AGAINST THEIR ORIGINAL DATA OF PDB ENTRY 3G61.
RfactorNum. reflection% reflection
Rfree0.2827 2804 9.93 %
Rwork0.2209 --
obs0.2271 28239 99.43 %
all-28400 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.35→19.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18367 0 106 0 18473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00518823
X-RAY DIFFRACTIONf_angle_d0.85325457
X-RAY DIFFRACTIONf_dihedral_angle_d12.086838
X-RAY DIFFRACTIONf_chiral_restr0.0582923
X-RAY DIFFRACTIONf_plane_restr0.0033235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.35-4.42420.35151240.31161236X-RAY DIFFRACTION94
4.4242-4.50380.34561380.27641196X-RAY DIFFRACTION98
4.5038-4.58940.32451270.27071262X-RAY DIFFRACTION99
4.5894-4.68190.35421350.26581246X-RAY DIFFRACTION100
4.6819-4.78230.32561390.24971269X-RAY DIFFRACTION100
4.7823-4.8920.34211540.25381245X-RAY DIFFRACTION100
4.892-5.01240.33521270.24341277X-RAY DIFFRACTION100
5.0124-5.14570.30791310.24021270X-RAY DIFFRACTION100
5.1457-5.29440.28491420.24031242X-RAY DIFFRACTION100
5.2944-5.46190.36841420.24271275X-RAY DIFFRACTION100
5.4619-5.65280.30581500.25161243X-RAY DIFFRACTION100
5.6528-5.87360.33321490.2681268X-RAY DIFFRACTION100
5.8736-6.13350.32031400.2621290X-RAY DIFFRACTION100
6.1335-6.44650.29981290.25141280X-RAY DIFFRACTION100
6.4465-6.83510.32151410.23651283X-RAY DIFFRACTION100
6.8351-7.33840.29181500.23031276X-RAY DIFFRACTION100
7.3384-8.03280.30811440.19871291X-RAY DIFFRACTION100
8.0328-9.09740.22571480.16961297X-RAY DIFFRACTION100
9.0974-11.12130.23221550.1611315X-RAY DIFFRACTION100
11.1213-19.95410.25681390.23261374X-RAY DIFFRACTION99
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)
10.84-0.08470.7979-1.66621.26232.64420.3214-0.2398-0.52560.4065-1.05950.12371.1963-0.9315-0.01342.35580.00690.37831.4965-0.50961.924336.740851.54435.5671
21.2988-0.2972-0.30790.89770.52872.32140.31550.0265-0.1085-0.3049-0.15870.040.0454-0.3499-0.00042.0397-0.1970.28581.5858-0.00891.656927.2176.587214.0559
32.17242.6706-0.0734.0541-0.5771.72660.5386-0.61040.2097-0.1466-0.47-0.2445-0.81320.6779-0.00082.1312-0.31730.1321.6335-0.33271.627845.224592.988455.8697
4-0.07880.0349-0.09660.08280.29490.39260.2235-3.54984.21542.1694-1.8241.77241.4181-1.1066-0.00013.0285-0.38860.09952.5461-1.17783.198341.8622117.597558.3269
53.9431.45391.66561.9462.08520.4158-3.5708-7.8958-1.47872.38273.54780.077-1.0912-5.81980.2218-1.2225-4.5065-0.1466-3.4718-0.57551.96165.001359.335611.2999
63.7576-1.7887-4.18870.09620.66965.6107-0.3320.5777-0.3918-0.75960.15980.8304-1.1132-0.230.00221.9035-0.37620.01351.3998-0.05491.95694.920266.0313.1913
7-0.7306-0.994-0.34753.40540.1594-0.0723-0.3457-0.15270.03030.24650.07410.66590.19580.8318-0.00031.8949-0.45080.35931.24220.11241.914131.992457.014423.7912
80.2635-0.9882-0.76830.78531.39631.1360.8542.0391-0.45390.13251.2349-2.2655-3.91191.85120.05062.6762-0.4747-0.10932.756-0.76062.251611.826157.115713.3458
91.91943.0922-0.19783.5386-1.02571.85871.4972-1.31651.44240.6167-2.03030.7478-0.88270.11450.00172.3209-0.47410.57922.0583-0.59782.361-8.219185.277851.7713
100.6947-0.28350.66740.0802-0.13090.70850.72491.1899-1.7397-2.1865-1.07341.1123-2.69591.364702.21730.0860.2222.4649-0.60572.45450.412892.651263.8816
110.01820.3372-0.4797-0.9364-1.3521-0.74680.4608-0.43070.74080.3656-0.33380.5264-0.47220.2417-0.00012.8482-0.35250.55451.9154-0.62282.31620.3248102.129851.3018
121.50220.43610.69731.62650.17681.37690.8597-0.28921.58110.48740.11271.0184-0.5081-0.055-0.00051.47650.21960.36741.39330.0812.074519.985556.242785.0281
131.01750.28860.1513-0.16730.00020.4728-0.7818-0.1332-3.32253.0290.6579-2.1411-0.0994-0.09420.02772.0775-0.17820.56031.34490.00682.564355.019654.520867.775
141.34851.22950.17159.20422.65210.72661.2643-0.71031.35584.33040.1166-1.99561.2981-1.0150.52350.9540.84390.57183.25790.53281.546426.707453.117692.7427
151.1501-3.83260.2948-2.83781.20380.1266-0.2753-1.0056-2.5275-0.5659-1.4141.6221-0.77540.29350.01652.2851-0.65710.39572.9757-0.3912.084346.827329.164883.1781
161.5553-0.2374-1.30821.4666-0.47380.72080.052-0.129-0.1150.2762-0.051-0.189-0.3325-0.1121-0.00011.714-0.27190.07912.3696-0.02131.526857.270653.909665.6758
171.60751.23734.41132.04493.42.01342.2187-2.34061.37911.0571-3.24982.12712.7632-1.88170.17571.19850.37550.24012.3271-0.58193.300760.555156.499939.4495
182.4851-1.75061.25330.3447-0.72530.1898-0.0444-0.69720.5387-0.3463-0.4456-1.35120.40360.3667-01.82680.13670.47331.8157-0.26542.208684.475458.459541.9099
190.4885-2.0857-1.7184-0.12510.50323.1438-0.13150.9726-0.66190.02770.01010.36460.8597-1.1489-0.00081.7051-0.44010.4711.9760.05482.563126.025122.660882.5419
202.4111-2.7163-0.0751-1.10180.0181-0.04312.4687-0.71781.29280.0663-0.0607-0.9978-1.74680.2620.00342.6545-0.2380.19822.0605-0.67062.400635.106727.023468.146
210.46660.7996-0.27750.80830.840.9153.1594-0.9672-0.577-2.91540.20942.2858-0.3291-0.88970.35271.2636-0.3161-0.68182.95360.13423.610119.059644.494469.8752
220.1447-0.3477-0.6568-0.07390.4751.12-0.3564-1.73460.97270.81871.39061.5129-0.7766-0.33710.00121.4687-0.2008-0.0692.00990.15032.178851.22161.952156.0526
232.3076-0.85071.32980.3328-0.43851.29940.4816-0.00420.61880.35721.03030.2518-1.3588-2.30540.02521.7561-0.2107-0.24742.29860.17231.836214.07351.060977.5572
240.174-0.7591-0.5577-1.74150.35040.5071-1.2344-0.9643-0.22480.37190.2346-0.74140.85530.97420.00582.07580.48280.75922.61340.3682.861820.854333.221777.0585
256.129-2.3983-2.42352.2303-1.80231.7416-0.3351-0.1719-0.5096-0.1210.2717-0.1295-0.31430.7120.00042.4461-0.23840.27242.3573-0.47631.981770.473814.99350.6474
260.8011.00260.18410.4035-0.03420.2763-1.94260.8255-2.2501-1.86983.0551-3.2936-0.46341.1515-0.00172.0594-0.6480.64872.8222-0.56413.274384.03718.064148.6505
270.4599-0.17230.4451-0.05870.28180.94432.13951.6575-1.0648-0.7277-1.72060.3082-1.2458-2.1408-0.0032.6471-0.95840.60014.07590.69931.97384.696327.335731.3711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 30:153)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 154:401)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 402:595)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 596:626)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 681:740)
6X-RAY DIFFRACTION6CHAIN A AND (RESID 741:851)
7X-RAY DIFFRACTION7CHAIN A AND (RESID 852:966)
8X-RAY DIFFRACTION8CHAIN A AND (RESID 967:1008)
9X-RAY DIFFRACTION9CHAIN A AND (RESID 1009:1044)
10X-RAY DIFFRACTION10CHAIN A AND (RESID 1045:1071)
11X-RAY DIFFRACTION11CHAIN A AND (RESID 1072:1271)
12X-RAY DIFFRACTION12CHAIN B AND (RESID 31:153)
13X-RAY DIFFRACTION13CHAIN B AND (RESID 154:183)
14X-RAY DIFFRACTION14CHAIN B AND (RESID 184:208)
15X-RAY DIFFRACTION15CHAIN B AND (RESID 209:263)
16X-RAY DIFFRACTION16CHAIN B AND (RESID 264:517)
17X-RAY DIFFRACTION17CHAIN B AND (RESID 518:542)
18X-RAY DIFFRACTION18CHAIN B AND (RESID 543:626)
19X-RAY DIFFRACTION19CHAIN B AND (RESID 688:794)
20X-RAY DIFFRACTION20CHAIN B AND (RESID 795:851)
21X-RAY DIFFRACTION21CHAIN B AND (RESID 852:884)
22X-RAY DIFFRACTION22CHAIN B AND (RESID 885:926)
23X-RAY DIFFRACTION23CHAIN B AND (RESID 927:961)
24X-RAY DIFFRACTION24CHAIN B AND (RESID 962:1008)
25X-RAY DIFFRACTION25CHAIN B AND (RESID 1009:1187)
26X-RAY DIFFRACTION26CHAIN B AND (RESID 1188:1237)
27X-RAY DIFFRACTION27CHAIN B AND (RESID 1238:1271)

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