PDB-5koy: Mouse pgp 34 linker deleted bound with ATP

ID or keywords:

Entry

Database: PDB / ID: 5koy

Title

Mouse pgp 34 linker deleted bound with ATP

Components

Multidrug resistance protein 1A

Keywords

HYDROLASE / Mouse pgp / multidrug resistance / drug transport / ATP bound

Function / homology

Function and homology information

Atorvastatin ADME / neural tissue regeneration / aldosterone secretion / Prednisone ADME / terpenoid transport / ceramide floppase activity / phosphatidylethanolamine floppase activity / carboxylic acid transmembrane transport / regulation of chloride transport / floppase activity ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.85 Å

Authors

Xia, D. / Esser, L. / Zhou, F.

Citation

Journal: J. Biol. Chem. / Year: 2017
Title: Structures of the Multidrug Transporter P-glycoprotein Reveal Asymmetric ATP Binding and the Mechanism of Polyspecificity.
Authors: Esser, L. / Zhou, F. / Pluchino, K.M. / Shiloach, J. / Ma, J. / Tang, W.K. / Gutierrez, C. / Zhang, A. / Shukla, S. / Madigan, J.P. / Zhou, T. / Kwong, P.D. / Ambudkar, S.V. / Gottesman, M.M. / Xia, D.

History

Deposition	Jul 1, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 14, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 25, 2017	Group: Database references
Revision 1.2	Oct 4, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5koy.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb5koy.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	5koy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ko/5koy ftp://data.pdbj.org/pub/pdb/validation_reports/ko/5koy	HTTPS FTP

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Related structure data

Related structure data	5ko2C 5kpdSC 5kpiC 5kpjC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3g5u-1 4m1m-1 4m1m-2 3g5u-2 4lsg-2 3g61-2 5kpd-2 5ko2-2 4lsg-1 4m2s-2 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 (14) #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

277 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
138 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
138 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	97.520, 116.439, 375.052
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: 137793.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abcb1a, Abcb4, Mdr1a, Mdr3, Pgy-3, Pgy3 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P21447, EC: 3.6.3.44
#2: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM

#1: Protein

Multidrug resistance protein 1A / ATP-binding cassette sub-family B member 1A / MDR1A / Multidrug resistance protein 3 / P-glycoprotein 3

Mass: 137793.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Abcb1a, Abcb4, Mdr1a, Mdr3, Pgy-3, Pgy3 / Production host:

Komagataella phaffii GS115 (fungus) / References: UniProt: P21447, EC: 3.6.3.44

#2: Chemical

ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE

Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.86 Å³/Da / Density % sol: 68.16 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 100 mM glycine pH 9.0, 150 mM NaCl, 31% PEG400. After crystals grew, crystals were soaked in cryoprotectant solution with 18 mM ATP

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2014

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 3.8→34.724 Å / Num. obs: 42251 / % possible obs: 99.9 % / Redundancy: 14.5 % / B_iso Wilson estimate: 150.45 Å² / R_merge(I) obs: 0.132 / R_pim(I) all: 0.035 / R_rim(I) all: 0.131 / Χ²: 0.987 / Net I/av σ(I): 18.667 / Net I/σ(I): 6.1 / Num. measured all: 611650

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	CC_1/2	Diffraction-ID	% possible all
3.8-3.87	9.5	0.997	0.372	1	99.5
3.87-3.94	10.3	0.98	0.508	1	99.9
3.94-4.01	11.2	0.887	0.619	1	99.9
4.01-4.09	11.8	0.793	0.725	1	100
4.09-4.18	12.5	0.7	0.829	1	100
4.18-4.28	12.9	0.613	0.897	1	100
4.28-4.39	13.5	0.51	0.934	1	100
4.39-4.5	14.2	0.43	0.957	1	100
4.5-4.64	14.6	0.374	0.971	1	100
4.64-4.79	15.1	0.348	0.976	1	100
4.79-4.96	15.4	0.32	0.984	1	100
4.96-5.16	15.7	0.303	0.984	1	100
5.16-5.39	16.1	0.295	0.986	1	100
5.39-5.67	16.2	0.29	0.985	1	100
5.67-6.03	16.3	0.267	0.987	1	100
6.03-6.49	16.6	0.214	0.993	1	100
6.49-7.15	16.9	0.162	0.994	1	100
7.15-8.18	17.1	0.112	0.997	1	100
8.18-10.29	17.3	0.08	0.998	1	100
10.29-50	15.9	0.067	0.998	1	99

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
DENZO		data reduction
SCALEPACK		data scaling
PDB_EXTRACT	3.2	data extraction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5KPD

5kpd

Resolution: 3.85→21.302 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2888	1951	4.74 %
R_work	0.246	-	-
obs	0.2481	41144	99.94 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.85→21.302 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18320	0	62	0	18382

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	18724
X-RAY DIFFRACTION	f_angle_d	1.031	25329
X-RAY DIFFRACTION	f_dihedral_angle_d	13.467	11149
X-RAY DIFFRACTION	f_chiral_restr	0.054	2916
X-RAY DIFFRACTION	f_plane_restr	0.006	3207

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 (%)
3.8501-3.9458	0.3957	136	0.3476	2743	X-RAY DIFFRACTION	100
3.9458-4.0517	0.36	137	0.3275	2757	X-RAY DIFFRACTION	100
4.0517-4.1701	0.3279	138	0.3063	2769	X-RAY DIFFRACTION	100
4.1701-4.3036	0.3118	137	0.2801	2771	X-RAY DIFFRACTION	100
4.3036-4.4561	0.3232	139	0.2617	2764	X-RAY DIFFRACTION	100
4.4561-4.6328	0.2682	137	0.2507	2773	X-RAY DIFFRACTION	100
4.6328-4.8413	0.2903	139	0.2417	2771	X-RAY DIFFRACTION	100
4.8413-5.0932	0.2836	137	0.2417	2776	X-RAY DIFFRACTION	100
5.0932-5.4074	0.3138	140	0.258	2808	X-RAY DIFFRACTION	100
5.4074-5.8171	0.3307	140	0.2787	2797	X-RAY DIFFRACTION	100
5.8171-6.3881	0.3209	138	0.2781	2788	X-RAY DIFFRACTION	100
6.3881-7.2799	0.3091	142	0.2562	2849	X-RAY DIFFRACTION	100
7.2799-9.0533	0.2322	143	0.219	2868	X-RAY DIFFRACTION	100
9.0533-21.3019	0.2606	148	0.2064	2959	X-RAY DIFFRACTION	100

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	0.93	-0.3913	-1.2542	2.4047	-2.6344	5.2061	-0.3189	1.1332	-0.6194	0.5882	-0.155	0.8097	0.197	0.7497	-1.5144	0.7864	-0.0041	0.4092	1.2917	-0.8343	1.3801	40.2499	58.4524	5.6137
2	7.6285	-1.0687	6.5259	1.5076	-0.8059	5.6036	1.8824	-0.3131	-0.3699	1.3231	0.0659	0.2169	1.7086	0.5816	2.8812	2.9981	-0.2849	0.8787	1.4902	-0.5272	2.083	19.9782	25.9085	-17.5505
3	0.4605	-0.4899	-0.6686	1.4338	1.7281	0.9161	0.1154	0.1041	-0.3935	-0.3137	-0.3544	-0.4797	0.1567	0.5625	-0.2844	1.6365	-0.2008	0.2255	1.3804	-0.3001	1.4498	38.4609	64.5451	15.5907
4	7.617	-1.9482	-4.2354	5.9401	0.6068	3.9782	-0.6201	-0.7872	0.8171	1.4565	0.7315	0.6638	0.8357	-0.3529	-2.5891	2.6536	-1.0888	0.1349	1.091	0.3724	0.7584	23.3037	70.3015	-6.2528
5	1.6373	-2.7332	-3.0248	4.5412	5.7248	5.8886	0.9064	1.1034	-0.6229	-2.3228	-1.2262	0.8336	-2.0454	-1.3311	-0.008	2.0203	-0.0855	0.3048	1.3174	-0.1066	1.5764	9.4522	76.4014	9.6034
6	2.1055	-0.0588	-0.0189	0.0491	0.9111	1.722	0.7151	0.0559	0.0859	0.2964	-0.5682	-0.4994	-0.0324	-0.0796	-0.0811	2.4023	-0.1257	0.2691	1.8133	-0.2443	1.5749	44.8909	91.6284	31.0941
7	4.1312	1.3746	0.2555	5.6943	-0.6104	3.2892	0.1036	-0.2865	-0.4509	-0.1949	0.2321	-0.1447	-0.9775	0.0996	0.0002	1.7147	-0.3927	-0.0325	1.2495	-0.2891	1.4355	45.1972	90.0411	56.2771
8	1.1531	-0.2897	0.1384	0.8352	0.7902	1.5055	-0.3213	0.1039	0.1319	-0.4811	-0.1837	0.7161	-0.2084	-0.456	-0.0006	1.0962	-0.2675	0.1331	0.8712	-0.0137	0.5078	21.4607	88.3681	35.6637
9	4.8245	0.6587	-0.0594	0.4015	0.2684	0.0125	0.4877	1.737	-0.8836	-0.7722	-2.4189	2.0548	-0.9376	-1.7289	-0.1555	2.268	-0.2206	-0.1354	1.6109	-0.5728	1.5533	9.0096	55.5098	-11.632
10	1.8477	-2.922	-0.2033	3.2362	1.5063	4.2092	0.0532	0.0336	-0.2598	-0.7011	-0.0905	0.4822	-0.4825	0.2445	0	1.3147	-0.4209	0.2218	1.1984	-0.1652	1.7388	9.3397	64.3371	21.2236
11	0.9984	-1.1412	0.81	1.5263	0.1883	3.1888	0.0201	0.4016	-0.3494	1.5457	0.6971	-0.4835	1.3509	1.0303	0.0111	1.0745	-0.3027	0.4503	1.1821	-0.0899	1.5268	36.3347	61.9722	26.578
12	0.1241	0.3629	0.7772	0.9433	1.2685	2.9541	0.0415	0.2888	-0.9182	-0.3192	0.2906	0.447	-0.0882	0.922	-0.0002	2.038	-0.0055	-0.0432	1.6248	-0.4108	1.7178	8.9318	60.0354	16.6752
13	2.5822	-1.5349	-1.3631	0.8181	0.0755	2.4187	0.3287	-0.845	-1.6222	0.1826	-0.2353	0.3455	-0.5576	0.3814	0.0757	1.8815	-0.2024	0.2358	1.4927	-0.2421	1.7794	-4.187	93.0052	52.4332
14	2.2448	-0.4425	2.162	2.1891	-2.9054	5.8164	1.4244	0.0452	-1.1392	0.6252	-1.0259	1.3729	-0.061	1.788	-0.1676	1.8732	-0.3878	0.6277	0.5271	-0.539	1.0025	2.4004	110.4612	44.029
15	1.9324	0.4676	0.4892	3.6028	1.0615	1.912	-0.3688	1.1352	-1.6316	-0.8368	0.6604	-1.572	0.3413	0.5054	-1.09	2.8312	-1.8216	0.7117	1.2979	-1.0075	2.5054	8.8986	106.9346	62.7163
16	1.3011	0.6454	0.4272	0.4964	-0.1426	0.4139	0.7099	-0.3609	1.111	-0.4862	-1.6031	0.1971	0.6161	-0.1069	-0.0118	1.7411	0.0181	0.4136	1.9944	-0.5498	1.3132	6.6251	102.0436	72.0769
17	0.1088	0.2584	0.1874	-0.0892	-0.8893	2.1519	1.6674	0.6417	0.5862	0.9443	-0.5523	0.1689	-1.381	-0.408	0.0585	1.3506	-0.0919	0.5415	1.546	-0.2925	1.5388	25.1002	58.5884	87.285
18	3.5771	0.6574	-1.9511	1.651	-0.0727	1.5912	0.2632	-0.2775	-0.213	0.2318	0.1588	-0.0142	0.1297	0.0944	-0.0001	1.2888	-0.0157	-0.0195	1.3755	0.3755	1.3307	27.4824	56.1536	78.3584
19	1.6369	1.9294	-1.1849	2.3954	-2.4666	3.4564	-0.0215	0.3984	0.2836	-0.6825	0.0728	-1.3115	1.8601	-0.8296	0.0076	1.3531	-0.2042	0.2275	1.9049	-0.1057	1.5146	29.7315	48.0839	94.9359
20	3.6484	-3.974	-1.6427	3.5369	-1.0594	2.299	-0.5567	-1.8927	-0.513	0.146	0.6429	1.2217	-0.933	1.7161	0.1069	1.7247	-0.4568	0.3604	2.3971	-0.3159	2.1261	49.2286	22.1171	76.7404
21	3.3977	2.2334	-3.2257	0.3139	-1.0136	1.9147	-0.8639	-1.1017	-1.6153	-0.0584	-0.2948	-0.388	0.7567	1.4822	-0.0905	1.2026	0.105	0.2956	1.9779	0.4177	1.9345	28.9032	47.3815	92.8816
22	3.7231	1.9007	0.966	4.4501	0.2664	6.0312	-0.047	-0.3817	0.2549	-0.0603	0.0635	-0.5326	-0.6346	-0.2564	0.0002	1.1733	-0.1026	0.2995	1.5595	-0.123	1.4347	72.8157	67.6563	51.9829
23	3.9719	-0.2387	0.955	0.2502	-1.0347	2.0619	-0.1991	0.6405	0.1917	-0.6492	-0.3568	0.6539	-0.4713	-0.0472	0.0003	1.2689	-0.033	0.2272	1.3763	-0.0345	1.5057	68.7355	60.4341	38.4767
24	1.7097	0.5473	-0.3995	0.069	-0.3342	0.18	-0.9045	-0.1854	-0.5672	-0.7699	-0.401	-0.0845	0.5396	-0.5775	-0.0129	1.6656	0.4587	0.5605	1.9815	-0.2335	1.9178	85.2987	53.247	45.1995
25	4.9844	-1.3354	-0.5834	1.1275	-0.9544	1.8519	-0.2947	-1.7739	-0.0647	0.0301	1.0772	-0.9728	-0.2085	-0.0534	-0.1576	1.1851	-0.6891	0.3625	1.1424	0.3255	2.043	19.12	23.8349	84.4596
26	1.9742	7.9694	0.4174	6.4328	-0.3863	1.5744	-0.0935	-2.1414	1.652	2.3851	-0.7943	3.4236	-0.513	-1.5295	-13.8898	1.2261	-0.3069	0.6561	0.4299	1.6783	1.647	15.3833	26.6653	100.3473
27	2.7709	-2.4916	-2.9557	1.5927	1.5775	3.7583	-0.046	-0.1713	-0.2529	0.052	0.4109	0.1835	-0.0007	-0.4218	-0.0001	1.3688	-0.4009	0.1081	1.4146	-0.0945	1.721	31.9416	29.1393	70.057
28	4.2723	-0.1101	-3.3522	0.0203	-1.6586	2.6318	-0.7268	0.9281	-1.6029	0.0089	0.468	-0.519	0.2717	-0.7997	0.0085	1.4329	-0.2748	0.2182	1.698	-0.0937	1.7118	27.9437	52.6691	70.6161
29	1.7459	-0.6882	1.8993	1.3782	0.6555	4.1249	-0.755	-0.1452	-0.913	-0.4328	-0.1946	0.6349	0.1542	0.9791	-0.0007	2.0032	-0.5212	0.3937	2.084	-0.2121	1.9934	62.429	17.4065	47.4449
30	1.986	0.8474	5.322	2.8776	-5.0447	1.9871	-2.4696	-1.7634	1.879	1.1827	-2.4815	0.4417	-0.3308	2.2863	-9.5316	1.2551	0.3575	-0.2332	3.5087	-0.9457	2.4616	82.5855	8.9795	66.5126
31	1.5735	-0.0149	3.2639	0.0808	0.7019	1.9749	-0.5513	0.0085	-0.5746	-0.1234	0.2074	0.4733	-3.2669	1.4507	-0.1223	1.4082	-0.7424	0.0204	3.0175	0.191	1.677	76.7889	17.4622	60.0217
32	7.7196	-1.3702	-1.4372	0.9142	1.1868	8.2308	-0.4067	1.663	1.8864	-0.9541	0.257	0.1061	-1.6551	-0.4738	-2.1482	1.052	-0.7918	0.7037	3.0176	-0.5812	1.0334	85.3059	23.4419	40.7279

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 31:81)
2	X-RAY DIFFRACTION	2	(chain A and resid 82:99)
3	X-RAY DIFFRACTION	3	(chain A and resid 100:203)
4	X-RAY DIFFRACTION	4	(chain A and resid 204:237)
5	X-RAY DIFFRACTION	5	(chain A and resid 238:327)
6	X-RAY DIFFRACTION	6	(chain A and resid 328:431)
7	X-RAY DIFFRACTION	7	(chain A and resid 432:581)
8	X-RAY DIFFRACTION	8	(chain A and resid 582:731)
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25	X-RAY DIFFRACTION	25	(chain B and resid 694:743)
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31	X-RAY DIFFRACTION	31	(chain B and resid 1162:1198)
32	X-RAY DIFFRACTION	32	(chain B and resid 1199:1271)

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