PDB-5ko2: Mouse pgp 34 linker deleted mutant Hg derivative

ID or keywords:

Entry

Database: PDB / ID: 5ko2

Title

Mouse pgp 34 linker deleted mutant Hg derivative

Components

Multidrug resistance protein 1A

Keywords

HYDROLASE / Mouse pgp / multidrug resistance / drug transport / Mercury derivative

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 / negative regulation of sensory perception of pain / regulation of intestinal absorption ...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 / negative regulation of sensory perception of pain / regulation of intestinal absorption / response to quercetin / cellular response to external biotic stimulus / response to antineoplastic agent / positive regulation of establishment of Sertoli cell barrier / Prednisone ADME / terpenoid transport / ceramide floppase activity / response to glycoside / floppase activity / ceramide translocation / establishment of blood-retinal barrier / protein localization to bicellular tight junction / response to alcohol / ABC-family proteins mediated transport / 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 / cellular response to L-glutamate / intercellular canaliculus / export across plasma membrane / ABC-type xenobiotic transporter / response to vitamin D / P-type phospholipid transporter / response to vitamin A / ABC-type xenobiotic transporter activity / intestinal absorption / response to glucagon / 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 / cellular response to estradiol stimulus / response to progesterone / female pregnancy / brush border membrane / placenta development / circadian rhythm / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to hypoxia / response to xenobiotic stimulus / apical plasma membrane / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.3 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	Jun 29, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 30, 2016	Provider: repository / Type: Initial release
Revision 1.1	Dec 21, 2016	Group: Database references
Revision 1.2	Jan 25, 2017	Group: Data collection / Database references
Revision 1.3	Sep 27, 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	5ko2.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb5ko2.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	5ko2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ko2_validation.pdf.gz	459 KB	Display	wwPDB validaton report
Full document	5ko2_full_validation.pdf.gz	481.9 KB	Display
Data in XML	5ko2_validation.xml.gz	74.4 KB	Display
Data in CIF	5ko2_validation.cif.gz	100.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ko/5ko2 ftp://data.pdbj.org/pub/pdb/validation_reports/ko/5ko2	HTTPS FTP

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Related structure data

Related structure data	5koyC 5kpdC 5kpiC 5kpjC 4m1mS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4m2s-2 4m1m-2 5koy-2 3g60-2 3g5u-2 4lsg-1 5uar-d 4m2t-2 3g5u-1 3g60-1 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) #147 - Mar 2012 Rhodopsin similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #224 - Aug 2018 Legumain similarity (1) #225 - Sep 2018 Phytase similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #27 - Mar 2002 Bacteriorhodopsin similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1) #58 - Oct 2004 G Proteins similarity (1) #66 - Jun 2005 Carotenoid Oxygenase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

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)
#147 - Mar 2012
Rhodopsin
similarity (1)
#100 - Apr 2008
Adrenergic Receptors
similarity (1)
#156 - Dec 2012
ABO Blood Type Glycosyltransferases
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#196 - Apr 2016
Lead Poisoning
similarity (1)
#224 - Aug 2018
Legumain
similarity (1)
#225 - Sep 2018
Phytase
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#27 - Mar 2002
Bacteriorhodopsin
similarity (1)
#49 - Jan 2004
Carbonic Anhydrase
similarity (1)
#58 - Oct 2004
G Proteins
similarity (1)
#66 - Jun 2005
Carotenoid Oxygenase
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Multidrug resistance protein 1A

B: Multidrug resistance protein 1A

hetero molecules

278 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
139 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
139 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	98.185, 114.741, 375.431
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 pastoris GS115 (fungus) / References: UniProt: P21447, xenobiotic-transporting ATPase
#2: Chemical	ChemComp-HG / MERCURY (II) ION Mass: 200.590 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Hg

#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 pastoris GS115 (fungus) / References: UniProt: P21447, xenobiotic-transporting ATPase

#2: Chemical

ChemComp-HG / MERCURY (II) ION

Mass: 200.590 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Hg

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.84 Å³/Da / Density % sol: 67.94 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein is pre-incubated with p-chloromercury phenylsulfonate to a final concentration of 4 mM of the organo mercury compound. To 10.5 ul of protein/organomercury, 3.5 ul of the precipitant ...Details: Protein is pre-incubated with p-chloromercury phenylsulfonate to a final concentration of 4 mM of the organo mercury compound. To 10.5 ul of protein/organomercury, 3.5 ul of the precipitant 25 mM HEPES 7.5 pH, 100 mM NaCl, 0.3 mM Cymal -7, 28% PEG400 was added. Reservoir: 50 mM HEPES 7.5pH, 100 mM NaCl and 30% PEG400.

Crystal

Density Matthews: 3.84 Å³/Da / Density % sol: 67.94 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein is pre-incubated with p-chloromercury phenylsulfonate to a final concentration of 4 mM of the organo mercury compound. To 10.5 ul of protein/organomercury, 3.5 ul of the precipitant ...

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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 27, 2016

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 3.3→49.109 Å / Num. obs: 114118 / % possible obs: 92.2 % / Redundancy: 11.5 % / B_iso Wilson estimate: 114.81 Å² / R_merge(I) obs: 0.148 / R_pim(I) all: 0.042 / R_rim(I) all: 0.154 / Χ²: 0.991 / Net I/av σ(I): 13.443 / Net I/σ(I): 9 / Num. measured all: 1309474

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	CC_1/2	Diffraction-ID	% possible all
3.3-3.38	8.3	0.968	0.217	1	89.4
3.38-3.46	9.2	0.905	0.302	1	90.5
3.46-3.55	9.8	0.829	0.474	1	91.1
3.55-3.66	10.3	0.694	0.67	1	91.4
3.66-3.78	10.7	0.6	0.78	1	91.4
3.78-3.91	11	0.479	0.886	1	92
3.91-4.07	11.3	0.372	0.939	1	91.8
4.07-4.25	11.7	0.282	0.967	1	91.7
4.25-4.48	12.1	0.219	0.982	1	92
4.48-4.76	12.4	0.175	0.988	1	92
4.76-5.13	12.5	0.158	0.99	1	91.7
5.13-5.64	12.6	0.149	0.99	1	92
5.64-6.46	12.8	0.141	0.991	1	92.4
6.46-8.13	13	0.106	0.996	1	96.1
8.13-50	14.1	0.104	0.994	1	97.6

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Processing

Software

Name	Version	Classification
PHENIX	dev_2443	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.2	data extraction
HKL-2000		data reduction
SHARP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4M1M

4m1m

Resolution: 3.3→33.536 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2848	3756	3.31 %	Random
R_work	0.243	-	-	-
obs	0.2444	113533	92.21 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.3→33.536 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18374	0	14	0	18388

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	18732
X-RAY DIFFRACTION	f_angle_d	0.664	25295
X-RAY DIFFRACTION	f_dihedral_angle_d	15.529	6807
X-RAY DIFFRACTION	f_chiral_restr	0.052	2914
X-RAY DIFFRACTION	f_plane_restr	0.004	3215

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 (%)
3.3-3.3417	0.3669	132	0.3589	3839	X-RAY DIFFRACTION	87
3.3417-3.3857	0.3481	133	0.3578	3997	X-RAY DIFFRACTION	90
3.3857-3.432	0.4258	136	0.3533	3970	X-RAY DIFFRACTION	91
3.432-3.481	0.3545	137	0.3529	3988	X-RAY DIFFRACTION	90
3.481-3.5329	0.3621	138	0.3393	4037	X-RAY DIFFRACTION	92
3.5329-3.588	0.3544	136	0.326	3990	X-RAY DIFFRACTION	90
3.588-3.6468	0.3493	143	0.3308	4054	X-RAY DIFFRACTION	92
3.6468-3.7096	0.3806	132	0.3052	4000	X-RAY DIFFRACTION	91
3.7096-3.777	0.32	143	0.3053	4124	X-RAY DIFFRACTION	92
3.777-3.8495	0.3663	135	0.2944	4020	X-RAY DIFFRACTION	92
3.8495-3.928	0.3157	135	0.2859	4094	X-RAY DIFFRACTION	92
3.928-4.0132	0.2787	134	0.2782	3972	X-RAY DIFFRACTION	92
4.0132-4.1064	0.2789	137	0.2577	4103	X-RAY DIFFRACTION	92
4.1064-4.209	0.2442	139	0.2497	4037	X-RAY DIFFRACTION	92
4.209-4.3225	0.273	143	0.238	4030	X-RAY DIFFRACTION	92
4.3225-4.4494	0.2427	140	0.2256	4100	X-RAY DIFFRACTION	92
4.4494-4.5927	0.2352	139	0.2068	4029	X-RAY DIFFRACTION	92
4.5927-4.7564	0.2178	139	0.204	4037	X-RAY DIFFRACTION	93
4.7564-4.9463	0.2095	138	0.2046	4087	X-RAY DIFFRACTION	92
4.9463-5.1706	0.2475	139	0.214	4074	X-RAY DIFFRACTION	92
5.1706-5.4422	0.316	134	0.2294	4015	X-RAY DIFFRACTION	92
5.4422-5.7815	0.3169	142	0.2497	4095	X-RAY DIFFRACTION	92
5.7815-6.2253	0.2742	138	0.2498	4022	X-RAY DIFFRACTION	93
6.2253-6.8469	0.2703	143	0.2338	4156	X-RAY DIFFRACTION	94
6.8469-7.8267	0.2739	144	0.2228	4266	X-RAY DIFFRACTION	97
7.8267-9.8196	0.2253	156	0.1815	4310	X-RAY DIFFRACTION	98
9.8196-33.5375	0.3177	151	0.2357	4331	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	0.7718	0.2898	-0.2448	3.552	1.0463	1.7668	0.2401	0.2418	0.0176	-1.0538	-0.3023	0.6627	0.1536	0.1306	-0.2555	1.0627	0.0669	-0.1708	0.4916	-0.3803	0.9802	36.2468	51.9032	5.5074
2	2.6647	0.2857	-0.4665	1.713	0.983	1.2769	0.2536	0.1881	0.5281	-0.5997	0.0856	-0.0253	-0.6734	-0.1555	-0.3008	1.246	-0.1254	0.0165	0.7213	0.0704	0.8768	19.7922	74.1283	9.6599
3	1.3346	1.278	0.9297	3.0193	2.141	1.5307	0.1653	-0.1177	0.0904	-0.1162	0.1054	-0.128	-0.4513	0.1479	-0.2797	1.2114	-0.0213	0.0438	0.885	-0.2321	1.1063	44.4544	88.5184	44.5204
4	1.3436	0.4844	0.1542	0.1946	0.1918	0.6854	0.0277	-0.0613	0.1821	0.2182	-0.1946	0.2318	0.1578	-0.215	0.1507	0.7707	-0.1234	-0.0084	0.4655	-0.1024	0.9397	19.9999	69.2401	23.61
5	0.3819	0.4197	0.0794	0.2213	0.0263	-0.0801	0.0071	-0.5002	-0.4177	0.1703	0.2005	0.4074	0.3981	0.4637	-0.232	1.1886	-0.1159	0.2336	1.044	-0.2931	1.1257	1.317	92.0426	46.3151
6	6.0476	2.9099	-3.1027	1.1092	-1.6839	2.0344	0.5001	-0.7109	0.6658	0.3164	0.0568	0.331	-0.5497	0.2487	-0.645	0.8276	0.0952	0.2781	1.2884	0.0329	1.121	20.8762	55.7073	84.3237
7	1.3093	0.2645	-0.8677	0.6186	-0.4968	1.5075	-0.0675	-0.0681	0.069	0.0021	0.1134	-0.0536	0.2447	0.0886	-0.0524	0.8885	-0.0368	0.165	1.1081	-0.0166	0.8705	52.7326	47.972	74.3532
8	6.5087	-1.6427	1.5982	4.7846	0.243	5.8379	-0.3916	1.1214	-0.6492	-0.4949	0.3831	0.105	-0.5311	0.3669	-0.0446	0.5607	0.0626	0.1902	0.7655	-0.0739	0.7234	64.933	62.2494	37.424
9	0.6258	-0.522	-0.1066	1.4943	-0.3099	0.8251	-0.1768	0.0023	-0.2962	-0.2008	0.1447	-0.1277	0.2661	-0.0412	-0.0225	0.9132	-0.1581	0.0454	0.9372	-0.1293	0.8374	37.9542	38.3078	68.8125
10	3.5256	-1.0733	-1.4111	1.5128	0.2593	0.778	0.1529	-0.7311	0.7308	-0.4007	0.1622	-0.2346	-0.1609	0.6194	-0.3301	1.0217	-0.2836	0.2455	1.3698	-0.209	0.927	66.9412	19.2876	52.1522

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 28 through 152 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 153 through 323 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 324 through 572 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 573 through 961 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 962 through 1272 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 28 through 153 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 154 through 479 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 480 through 581 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 582 through 961 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 962 through 1271 )

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