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

ID or keywords:

Entry

Database: PDB / ID: 4m2t

Title

Corrected Structure of Mouse P-glycoprotein bound to QZ59-SSS

Components

Multidrug resistance protein 1A

Keywords

HYDROLASE/HYDROLASE INHIBITOR / ATP-Binding Cassette Transporter / Multidrug Efflux / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

Function and homology information

hormone transport / cellular response to nonylphenol / 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 / negative regulation of sensory perception of pain ...hormone transport / cellular response to nonylphenol / 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 / negative regulation of sensory perception of pain / positive regulation of establishment of Sertoli cell barrier / regulation of intestinal absorption / response to quercetin / cellular response to external biotic stimulus / response to antineoplastic agent / Prednisone ADME / terpenoid transport / ceramide floppase activity / establishment of blood-retinal barrier / response to glycoside / protein localization to bicellular tight junction / ceramide translocation / floppase activity / ABC-family proteins mediated transport / response to thyroxine / establishment of blood-brain barrier / phosphatidylethanolamine flippase activity / phosphatidylcholine floppase activity / cellular response to L-glutamate / xenobiotic transport across blood-brain barrier / intercellular canaliculus / xenobiotic detoxification by transmembrane export across the plasma membrane / response to vitamin D / export across plasma membrane / P-type phospholipid transporter / ABC-type xenobiotic transporter / response to alcohol / response to vitamin A / response to glucagon / intestinal absorption / ABC-type xenobiotic transporter activity / cellular response to antibiotic / phospholipid translocation / cellular hyperosmotic salinity response / cellular response to alkaloid / maintenance of blood-brain barrier / efflux transmembrane transporter activity / transmembrane transporter activity / xenobiotic transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / response to cadmium ion / lactation / cellular response to dexamethasone stimulus / response to progesterone / female pregnancy / placenta development / cellular response to estradiol stimulus / brush border membrane / circadian rhythm / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to hypoxia / apical plasma membrane / response to xenobiotic stimulus / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 4.35 Å

Authors

Li, J. / Jaimes, K.F. / Aller, S.G.

Citation

Journal: Protein Sci. / Year: 2014
Title: Refined structures of mouse P-glycoprotein.
Authors: Li, J. / Jaimes, K.F. / Aller, S.G.

History

Deposition	Aug 5, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 13, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 1, 2014	Group: Database references
Revision 1.2	Feb 28, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4m2t.cif.gz	954.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4m2t.ent.gz	805 KB	Display	PDB format
PDBx/mmJSON format	4m2t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4m2t_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4m2t_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4m2t_validation.xml.gz	84.2 KB	Display
Data in CIF	4m2t_validation.cif.gz	111.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m2/4m2t ftp://data.pdbj.org/pub/pdb/validation_reports/m2/4m2t	HTTPS FTP

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Related structure data

Related structure data	4m1mC 4m2sC 3g5u 3g60 3g61 C: citing same article (ref.)
Similar structure data	3g61-1 5kpi-2 4m2s-1 5kpi-1 3g5u-1 3g60-1 4lsg-1 4m1m-1 5kpd-2 6h4v-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#123 - Mar 2010 P-glycoprotein similarity (15) #95 - Nov 2007 Multidrug Resistance Transporters similarity (10) #80 - Aug 2006 AAA+ Proteases similarity (1) #166 - Oct 2013 Proteasome similarity (1)

Deposited unit

A: Multidrug resistance protein 1A

B: Multidrug resistance protein 1A

hetero molecules

286 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Multidrug resistance protein 1A

hetero molecules

defined by author&software
143 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Multidrug resistance protein 1A

hetero molecules

defined by author&software
143 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Multidrug resistance protein 1A / 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, EC: 3.6.3.44
#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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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.73 Å³/Da / Density % sol: 66.99 %

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 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

Software

Name: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement

Refinement

Method 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.

	R_factor	Num. reflection	% reflection
R_free	0.2827	2804	9.93 %
R_work	0.2209	-	-
obs	0.2271	28239	99.43 %
all	-	28400	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 4.35→19.954 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18367	0	106	0	18473

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	18823
X-RAY DIFFRACTION	f_angle_d	0.853	25457
X-RAY DIFFRACTION	f_dihedral_angle_d	12.08	6838
X-RAY DIFFRACTION	f_chiral_restr	0.058	2923
X-RAY DIFFRACTION	f_plane_restr	0.003	3235

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
4.35-4.4242	0.3515	124	0.3116	1236	X-RAY DIFFRACTION	94
4.4242-4.5038	0.3456	138	0.2764	1196	X-RAY DIFFRACTION	98
4.5038-4.5894	0.3245	127	0.2707	1262	X-RAY DIFFRACTION	99
4.5894-4.6819	0.3542	135	0.2658	1246	X-RAY DIFFRACTION	100
4.6819-4.7823	0.3256	139	0.2497	1269	X-RAY DIFFRACTION	100
4.7823-4.892	0.3421	154	0.2538	1245	X-RAY DIFFRACTION	100
4.892-5.0124	0.3352	127	0.2434	1277	X-RAY DIFFRACTION	100
5.0124-5.1457	0.3079	131	0.2402	1270	X-RAY DIFFRACTION	100
5.1457-5.2944	0.2849	142	0.2403	1242	X-RAY DIFFRACTION	100
5.2944-5.4619	0.3684	142	0.2427	1275	X-RAY DIFFRACTION	100
5.4619-5.6528	0.3058	150	0.2516	1243	X-RAY DIFFRACTION	100
5.6528-5.8736	0.3332	149	0.268	1268	X-RAY DIFFRACTION	100
5.8736-6.1335	0.3203	140	0.262	1290	X-RAY DIFFRACTION	100
6.1335-6.4465	0.2998	129	0.2514	1280	X-RAY DIFFRACTION	100
6.4465-6.8351	0.3215	141	0.2365	1283	X-RAY DIFFRACTION	100
6.8351-7.3384	0.2918	150	0.2303	1276	X-RAY DIFFRACTION	100
7.3384-8.0328	0.3081	144	0.1987	1291	X-RAY DIFFRACTION	100
8.0328-9.0974	0.2257	148	0.1696	1297	X-RAY DIFFRACTION	100
9.0974-11.1213	0.2322	155	0.161	1315	X-RAY DIFFRACTION	100
11.1213-19.9541	0.2568	139	0.2326	1374	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.84	-0.0847	0.7979	-1.6662	1.2623	2.6442	0.3214	-0.2398	-0.5256	0.4065	-1.0595	0.1237	1.1963	-0.9315	-0.0134	2.3558	0.0069	0.3783	1.4965	-0.5096	1.9243	36.7408	51.5443	5.5671
2	1.2988	-0.2972	-0.3079	0.8977	0.5287	2.3214	0.3155	0.0265	-0.1085	-0.3049	-0.1587	0.04	0.0454	-0.3499	-0.0004	2.0397	-0.197	0.2858	1.5858	-0.0089	1.6569	27.21	76.5872	14.0559
3	2.1724	2.6706	-0.073	4.0541	-0.577	1.7266	0.5386	-0.6104	0.2097	-0.1466	-0.47	-0.2445	-0.8132	0.6779	-0.0008	2.1312	-0.3173	0.132	1.6335	-0.3327	1.6278	45.2245	92.9884	55.8697
4	-0.0788	0.0349	-0.0966	0.0828	0.2949	0.3926	0.2235	-3.5498	4.2154	2.1694	-1.824	1.7724	1.4181	-1.1066	-0.0001	3.0285	-0.3886	0.0995	2.5461	-1.1778	3.1983	41.8622	117.5975	58.3269
5	3.943	1.4539	1.6656	1.946	2.0852	0.4158	-3.5708	-7.8958	-1.4787	2.3827	3.5478	0.077	-1.0912	-5.8198	0.2218	-1.2225	-4.5065	-0.1466	-3.4718	-0.5755	1.9616	5.0013	59.3356	11.2999
6	3.7576	-1.7887	-4.1887	0.0962	0.6696	5.6107	-0.332	0.5777	-0.3918	-0.7596	0.1598	0.8304	-1.1132	-0.23	0.0022	1.9035	-0.3762	0.0135	1.3998	-0.0549	1.9569	4.9202	66.03	13.1913
7	-0.7306	-0.994	-0.3475	3.4054	0.1594	-0.0723	-0.3457	-0.1527	0.0303	0.2465	0.0741	0.6659	0.1958	0.8318	-0.0003	1.8949	-0.4508	0.3593	1.2422	0.1124	1.9141	31.9924	57.0144	23.7912
8	0.2635	-0.9882	-0.7683	0.7853	1.3963	1.136	0.854	2.0391	-0.4539	0.1325	1.2349	-2.2655	-3.9119	1.8512	0.0506	2.6762	-0.4747	-0.1093	2.756	-0.7606	2.2516	11.8261	57.1157	13.3458
9	1.9194	3.0922	-0.1978	3.5386	-1.0257	1.8587	1.4972	-1.3165	1.4424	0.6167	-2.0303	0.7478	-0.8827	0.1145	0.0017	2.3209	-0.4741	0.5792	2.0583	-0.5978	2.361	-8.2191	85.2778	51.7713
10	0.6947	-0.2835	0.6674	0.0802	-0.1309	0.7085	0.7249	1.1899	-1.7397	-2.1865	-1.0734	1.1123	-2.6959	1.3647	0	2.2173	0.086	0.222	2.4649	-0.6057	2.4545	0.4128	92.6512	63.8816
11	0.0182	0.3372	-0.4797	-0.9364	-1.3521	-0.7468	0.4608	-0.4307	0.7408	0.3656	-0.3338	0.5264	-0.4722	0.2417	-0.0001	2.8482	-0.3525	0.5545	1.9154	-0.6228	2.3162	0.3248	102.1298	51.3018
12	1.5022	0.4361	0.6973	1.6265	0.1768	1.3769	0.8597	-0.2892	1.5811	0.4874	0.1127	1.0184	-0.5081	-0.055	-0.0005	1.4765	0.2196	0.3674	1.3933	0.081	2.0745	19.9855	56.2427	85.0281
13	1.0175	0.2886	0.1513	-0.1673	0.0002	0.4728	-0.7818	-0.1332	-3.3225	3.029	0.6579	-2.1411	-0.0994	-0.0942	0.0277	2.0775	-0.1782	0.5603	1.3449	0.0068	2.5643	55.0196	54.5208	67.775
14	1.3485	1.2295	0.1715	9.2042	2.6521	0.7266	1.2643	-0.7103	1.3558	4.3304	0.1166	-1.9956	1.2981	-1.015	0.5235	0.954	0.8439	0.5718	3.2579	0.5328	1.5464	26.7074	53.1176	92.7427
15	1.1501	-3.8326	0.2948	-2.8378	1.2038	0.1266	-0.2753	-1.0056	-2.5275	-0.5659	-1.414	1.6221	-0.7754	0.2935	0.0165	2.2851	-0.6571	0.3957	2.9757	-0.391	2.0843	46.8273	29.1648	83.1781
16	1.5553	-0.2374	-1.3082	1.4666	-0.4738	0.7208	0.052	-0.129	-0.115	0.2762	-0.051	-0.189	-0.3325	-0.1121	-0.0001	1.714	-0.2719	0.0791	2.3696	-0.0213	1.5268	57.2706	53.9096	65.6758
17	1.6075	1.2373	4.4113	2.0449	3.4	2.0134	2.2187	-2.3406	1.3791	1.0571	-3.2498	2.1271	2.7632	-1.8817	0.1757	1.1985	0.3755	0.2401	2.3271	-0.5819	3.3007	60.5551	56.4999	39.4495
18	2.4851	-1.7506	1.2533	0.3447	-0.7253	0.1898	-0.0444	-0.6972	0.5387	-0.3463	-0.4456	-1.3512	0.4036	0.3667	-0	1.8268	0.1367	0.4733	1.8157	-0.2654	2.2086	84.4754	58.4595	41.9099
19	0.4885	-2.0857	-1.7184	-0.1251	0.5032	3.1438	-0.1315	0.9726	-0.6619	0.0277	0.0101	0.3646	0.8597	-1.1489	-0.0008	1.7051	-0.4401	0.471	1.976	0.0548	2.5631	26.0251	22.6608	82.5419
20	2.4111	-2.7163	-0.0751	-1.1018	0.0181	-0.0431	2.4687	-0.7178	1.2928	0.0663	-0.0607	-0.9978	-1.7468	0.262	0.0034	2.6545	-0.238	0.1982	2.0605	-0.6706	2.4006	35.1067	27.0234	68.146
21	0.4666	0.7996	-0.2775	0.8083	0.84	0.915	3.1594	-0.9672	-0.577	-2.9154	0.2094	2.2858	-0.3291	-0.8897	0.3527	1.2636	-0.3161	-0.6818	2.9536	0.1342	3.6101	19.0596	44.4944	69.8752
22	0.1447	-0.3477	-0.6568	-0.0739	0.475	1.12	-0.3564	-1.7346	0.9727	0.8187	1.3906	1.5129	-0.7766	-0.3371	0.0012	1.4687	-0.2008	-0.069	2.0099	0.1503	2.1788	51.221	61.9521	56.0526
23	2.3076	-0.8507	1.3298	0.3328	-0.4385	1.2994	0.4816	-0.0042	0.6188	0.3572	1.0303	0.2518	-1.3588	-2.3054	0.0252	1.7561	-0.2107	-0.2474	2.2986	0.1723	1.8362	14.073	51.0609	77.5572
24	0.174	-0.7591	-0.5577	-1.7415	0.3504	0.5071	-1.2344	-0.9643	-0.2248	0.3719	0.2346	-0.7414	0.8553	0.9742	0.0058	2.0758	0.4828	0.7592	2.6134	0.368	2.8618	20.8543	33.2217	77.0585
25	6.129	-2.3983	-2.4235	2.2303	-1.8023	1.7416	-0.3351	-0.1719	-0.5096	-0.121	0.2717	-0.1295	-0.3143	0.712	0.0004	2.4461	-0.2384	0.2724	2.3573	-0.4763	1.9817	70.4738	14.993	50.6474
26	0.801	1.0026	0.1841	0.4035	-0.0342	0.2763	-1.9426	0.8255	-2.2501	-1.8698	3.0551	-3.2936	-0.4634	1.1515	-0.0017	2.0594	-0.648	0.6487	2.8222	-0.5641	3.2743	84.037	18.0641	48.6505
27	0.4599	-0.1723	0.4451	-0.0587	0.2818	0.9443	2.1395	1.6575	-1.0648	-0.7277	-1.7206	0.3082	-1.2458	-2.1408	-0.003	2.6471	-0.9584	0.6001	4.0759	0.6993	1.973	84.6963	27.3357	31.3711

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 30:153)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 154:401)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 402:595)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 596:626)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 681:740)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 741:851)
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 852:966)
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 967:1008)
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESID 1009:1044)
10	X-RAY DIFFRACTION	10	CHAIN A AND (RESID 1045:1071)
11	X-RAY DIFFRACTION	11	CHAIN A AND (RESID 1072:1271)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 31:153)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 154:183)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 184:208)
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 209:263)
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESID 264:517)
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESID 518:542)
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESID 543:626)
19	X-RAY DIFFRACTION	19	CHAIN B AND (RESID 688:794)
20	X-RAY DIFFRACTION	20	CHAIN B AND (RESID 795:851)
21	X-RAY DIFFRACTION	21	CHAIN B AND (RESID 852:884)
22	X-RAY DIFFRACTION	22	CHAIN B AND (RESID 885:926)
23	X-RAY DIFFRACTION	23	CHAIN B AND (RESID 927:961)
24	X-RAY DIFFRACTION	24	CHAIN B AND (RESID 962:1008)
25	X-RAY DIFFRACTION	25	CHAIN B AND (RESID 1009:1187)
26	X-RAY DIFFRACTION	26	CHAIN B AND (RESID 1188:1237)
27	X-RAY DIFFRACTION	27	CHAIN B AND (RESID 1238:1271)

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