PDB-3srd: Human M2 pyruvate kinase in complex with fructose 1-6 bisphosphat...

ID or keywords:

Entry

Database: PDB / ID: 3srd

Title

Human M2 pyruvate kinase in complex with fructose 1-6 bisphosphate and Oxalate.

Components

Pyruvate kinase isozymes M1/M2

Keywords

TRANSFERASE /

TIM Barrel / Phosphoryl transfer / PEP Binding /

cytosol

Function / homology

Function and homology information

programmed cell death /

pyruvate kinase /

pyruvate kinase activity / positive regulation of cytoplasmic translation / histone H3T11 kinase activity / canonical glycolysis /

Glycolysis / positive regulation of sprouting angiogenesis /

potassium ion binding /

rough endoplasmic reticulum ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.902 Å

Authors

Morgan, H.P. / O'Reilly, F. / Palmer, R. / McNae, I.W. / Nowicki, M.W. / Wear, M.A. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.

Citation

Journal: To be Published
Title: Allosetric regulation of M2 pyruvate kinase.
Authors: Morgan, H.P. / O'Reilly, F. / Palmer, R. / McNae, I.W. / Nowicki, M.W. / Wear, M.A. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.

History

Deposition	Jul 7, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 8, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3srd.cif.gz	779.7 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sr/3srd ftp://data.pdbj.org/pub/pdb/validation_reports/sr/3srd	HTTPS FTP

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Related structure data

Related structure data	3srfC 3srhC C: citing same article (ref.)
Similar structure data	1f3w-2 2g50-2 1f3x-2 4g1n-d 5x0i-d 2vgi-d 1pkm-1 2vgb-d 3bjf-d 2g50-1 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	#50 - Feb 2004 Glycolytic Enzymes similarity (15) #102 - Jun 2008 Lactate Dehydrogenase similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1)

Deposited unit

A: Pyruvate kinase isozymes M1/M2

B: Pyruvate kinase isozymes M1/M2

C: Pyruvate kinase isozymes M1/M2

D: Pyruvate kinase isozymes M1/M2

hetero molecules

243 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	95.050, 117.370, 110.460
Angle α, β, γ (deg.)	90.00, 113.56, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	13 - 531
2	1	1	1	B	13 - 531
3	1	1	1	C	13 - 531
4	1	1	1	D	13 - 531

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein

Pyruvate kinase isozymes M1/M2 / Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate ...

Mass: 60188.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: OIP3, PK2, PK3, PKM, PKM2 / Plasmid: pET28a_M2 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14618,

pyruvate kinase

#3: Sugar

ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose /

Fructose 1,6-bisphosphate

Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₄O₁₂P₂

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Non-polymers , 5 types, 142 molecules

#2: Chemical	ChemComp-OXL / OXALATE ION / Oxalate Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂O₄
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.57 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 10-16% polyethyleneglycol 8000, 20 mM triethanolamine-HCl buffer (pH 7.2), 50 mM MgCl2, 100 mM KCl, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 1 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2011

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.9→58.7 Å / Num. all: 129300 / Num. obs: 45352 / % possible obs: 92 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 2.9 / Redundancy: 2.9 % / R_merge(I) obs: 0.062 / R_sym value: 0.088 / Net I/σ(I): 11.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	R_sym value	% possible all
2.9-2.98	2.3	0.549	31.8	3118	0.549	90
12.98-58.72	2.8	0.015	1.4	549	0.015	93

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Processing

Software

Name	Version	Classification
DNA		data collection
PHASER		phasing
REFMAC	5.5.0072	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.902→54.18 Å / Cor.coef. F_o:F_c: 0.903 / Cor.coef. F_o:F_c free: 0.882 / SU B: 55.204 / SU ML: 0.468 / Cross valid method: THROUGHOUT / ESU R Free: 0.503 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27899	2283	5 %	RANDOM
R_work	0.25298	-	-	-
obs	0.25431	43039	100 %	-
all	-	45322	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 78.245 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.59 Å²	0 Å²	0.6 Å²
2-	-	-0.05 Å²	0 Å²
3-	-	-	-0.06 Å²

Refinement step

Cycle: LAST / Resolution: 2.902→54.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15772	0	141	126	16039

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	16173
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.046	1.98	21852
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.498	5	2054
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.685	24.012	668
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.87	15	2919
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.324	15	124
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	2512
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	11908
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.276	1.5	10238
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.525	2	16522
X-RAY DIFFRACTION	r_scbond_it	0.578	3	5935
X-RAY DIFFRACTION	r_scangle_it	1.071	4.5	5330
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 3920 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	TIGHT POSITIONAL	0.03	0.05
2	B	TIGHT POSITIONAL	0.02	0.05
3	C	TIGHT POSITIONAL	0.03	0.05
4	D	TIGHT POSITIONAL	0.04	0.05
1	A	TIGHT THERMAL	0.03	0.5
2	B	TIGHT THERMAL	0.03	0.5
3	C	TIGHT THERMAL	0.03	0.5
4	D	TIGHT THERMAL	0.03	0.5

LS refinement shell

Resolution: 2.902→2.977 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.414	159	-
R_work	0.376	2949	-
obs	-	-	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	1.0562	1.4513	-1.2765	2.898	-1.8099	1.548	0.4971	0.1716	0.359	0.0159	-0.0894	0.7751	-0.5027	-0.2064	-0.4077	0.7005	0.1591	-0.027	0.501	0.0056	0.4547	-14.4459	9.4012	-15.0272
2	1.0449	0.2202	-0.3955	1.0503	-0.0981	1.4635	-0.0166	0.0338	0.1419	0.134	0.0158	-0.0233	-0.1679	-0.0714	0.0008	0.1526	0.0083	0.0685	0.1336	-0.0379	0.1517	-30.3724	-7.2543	9.4502
3	0.5408	-0.2287	-0.1045	0.4684	-0.388	1.1335	-0.0155	-0.0677	-0.1297	0.0533	0.0212	0.0382	0.2319	0.073	-0.0057	0.1893	0.0164	0.0508	0.1127	-0.0152	0.1397	-21.3283	-21.5186	7.8595
4	2.2898	0.3456	0.7058	1.5567	-0.2673	2.132	0.0449	0.1856	-0.0234	-0.1051	0.0192	0.0722	-0.0439	-0.1153	-0.0641	0.1826	0.0353	0.0823	0.1705	0.0276	0.1787	-36.7453	-0.4318	-14.9519
5	1.0369	0.9229	-2.4285	2.1617	-1.8754	5.7606	-0.0347	0.5163	0.2368	0.2017	0.2527	0.9716	0.7224	-1.2974	-0.218	0.5418	-0.1155	0.0483	0.6675	-0.0322	0.6215	-19.228	-14.5665	-37.699
6	0.6267	-0.0543	0.1257	0.679	-0.0869	0.7205	-0.0025	0.3806	0.3002	-0.2918	-0.0001	-0.1598	-0.2501	0.005	0.0026	0.4085	0.0827	0.1006	0.4007	0.0751	0.3805	-14.9276	14.9333	-65.8023
7	0.9361	-0.2403	-0.0164	0.3579	-0.2171	0.5106	0.0551	0.016	0.3486	0.028	0.0092	0.0382	-0.2922	-0.2224	-0.0643	0.3027	0.0817	0.0587	0.2798	0.0302	0.289	-17.953	11.4912	-53.9819
8	1.1082	-0.6224	-0.9561	1.8559	0.082	2.1237	0.1147	0.2391	-0.0005	-0.0901	-0.031	0.027	0.0355	-0.0914	-0.0837	0.2318	0.0579	0.0755	0.3049	0.0626	0.2539	-36.0581	2.7628	-38.188
9	1.0565	0.1821	0.2194	0.0393	0.0302	0.1171	0.03	-0.2177	-0.8253	-0.0666	0.0939	-0.1596	0.1935	0.1024	-0.1239	0.76	0.211	0.0133	0.6975	-0.0914	0.7516	-6.1238	-18.2214	-15.8691
10	0.8217	-0.1603	-0.184	0.7669	0.1526	0.5159	-0.041	-0.174	0.0642	0.196	0.0022	-0.0257	-0.0505	0.1434	0.0388	0.2999	-0.0238	0.0418	0.272	0.0049	0.2123	2.914	7.122	13.3579
11	1.4161	0.014	-0.2863	0.9866	0.3565	0.5584	-0.0008	-0.1452	-0.0505	0.1068	-0.0242	-0.0304	-0.0356	0.1819	0.025	0.1792	-0.0011	0.0428	0.1918	-0.0163	0.1585	-2.4454	-1.6232	3.3964
12	1.662	0.6653	-0.7913	2.0409	0.168	1.8177	0.0154	-0.0651	-0.0173	-0.0583	-0.0118	-0.1294	0.0691	0.1139	-0.0036	0.1854	0.013	0.0647	0.2319	0.0238	0.1925	15.9726	-9.1146	-13.5936
13	0.2864	0.482	-0.428	0.939	-0.7494	1.8868	0.096	-0.0532	-0.0065	0.066	-0.0629	-0.2948	-0.4736	0.5871	-0.0332	0.5698	0.0037	0.0503	0.57	-0.0202	0.6801	-1.1208	8.2096	-35.1444
14	1.1288	0.171	-0.0106	0.7012	0.0871	1.5742	-0.0458	0.1246	0.0895	-0.1093	-0.0046	0.1735	0.0742	-0.2502	0.0504	0.1751	0.025	0.0932	0.0958	0.0508	0.1511	-1.4366	-15.7336	-68.4766
15	1.5138	-0.1302	-0.229	0.6107	0.1504	1.448	0.0025	0.0233	-0.0828	-0.0408	0.0043	0.0688	0.1397	-0.059	-0.0068	0.1441	-0.0131	0.0631	0.1078	0.014	0.1317	1.0161	-15.1516	-55.8249
16	1.8144	0.019	0.5381	1.4279	-0.0361	2.3353	0.0002	-0.1724	0.014	0.1522	0.0232	0.027	-0.03	0.0253	-0.0234	0.1456	-0.0109	0.0809	0.126	0.022	0.1613	17.5169	-8.8926	-37.0702

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	13 - 26
2	X-RAY DIFFRACTION	2	A	27 - 134
3	X-RAY DIFFRACTION	3	A	135 - 382
4	X-RAY DIFFRACTION	4	A	383 - 531
5	X-RAY DIFFRACTION	5	B	14 - 25
6	X-RAY DIFFRACTION	6	B	26 - 225
7	X-RAY DIFFRACTION	7	B	226 - 387
8	X-RAY DIFFRACTION	8	B	388 - 531
9	X-RAY DIFFRACTION	9	C	13 - 26
10	X-RAY DIFFRACTION	10	C	27 - 279
11	X-RAY DIFFRACTION	11	C	280 - 381
12	X-RAY DIFFRACTION	12	C	382 - 531
13	X-RAY DIFFRACTION	13	D	15 - 27
14	X-RAY DIFFRACTION	14	D	28 - 219
15	X-RAY DIFFRACTION	15	D	220 - 388
16	X-RAY DIFFRACTION	16	D	389 - 531

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-Protein / Sugars , 2 types, 8 molecules ABCD

-Non-polymers , 5 types, 142 molecules

-Experimental details

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Protein / Sugars , 2 types, 8 molecules ABCD

-
Non-polymers , 5 types, 142 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi