PDB-6qu5: Crystal Structure of Phosphofructokinase from Trypanosoma brucei ...

ID or keywords:

Entry

Database: PDB / ID: 6qu5

Title

Crystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an allosteric inhibitor ctcb12

Components

ATP-dependent 6-phosphofructokinase

Keywords

TRANSFERASE / Glycolysis / Inhibitor / Allostery

Function / homology

Function and homology information

6-phosphofructokinase / 6-phosphofructokinase activity / glycosome / fructose 6-phosphate metabolic process / phosphate ion binding / glycolytic process / ATP binding / metal ion binding
Similarity search - Function

Biological species

Trypanosoma brucei brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.4 Å

Authors

McNae, I.W. / Dornan, J. / Walkinshaw, M.D.

Funding support

United Kingdom, 1items

Citation

Journal: Nat Commun / Year: 2021
Title: Fast acting allosteric phosphofructokinase inhibitors block trypanosome glycolysis and cure acute African trypanosomiasis in mice.
Authors: McNae, I.W. / Kinkead, J. / Malik, D. / Yen, L.H. / Walker, M.K. / Swain, C. / Webster, S.P. / Gray, N. / Fernandes, P.M. / Myburgh, E. / Blackburn, E.A. / Ritchie, R. / Austin, C. / Wear, M. ...

History

Deposition	Feb 26, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 30, 2020	Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2	Mar 3, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3	Jan 24, 2024	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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6qu5.cif.gz	1.4 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	6qu5_validation.pdf.gz	565.8 KB	Display	wwPDB validaton report
Full document	6qu5_full_validation.pdf.gz	644.7 KB	Display
Data in XML	6qu5_validation.xml.gz	127.2 KB	Display
Data in CIF	6qu5_validation.cif.gz	167.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qu/6qu5 ftp://data.pdbj.org/pub/pdb/validation_reports/qu/6qu5	HTTPS FTP

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Related structure data

Related structure data	6qu3C 6qu4C 3f5mS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6qu3-d 6qu4-d 3f5m-d 21354 2xf2-d 5zqt-d 2hig-1 2po1-1 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	#50 - Feb 2004 Glycolytic Enzymes similarity (5)

Deposited unit

A: ATP-dependent 6-phosphofructokinase

B: ATP-dependent 6-phosphofructokinase

C: ATP-dependent 6-phosphofructokinase

D: ATP-dependent 6-phosphofructokinase

E: ATP-dependent 6-phosphofructokinase

F: ATP-dependent 6-phosphofructokinase

G: ATP-dependent 6-phosphofructokinase

H: ATP-dependent 6-phosphofructokinase

hetero molecules

448 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ATP-dependent 6-phosphofructokinase

B: ATP-dependent 6-phosphofructokinase

C: ATP-dependent 6-phosphofructokinase

D: ATP-dependent 6-phosphofructokinase

hetero molecules

defined by author&software
Evidence: gel filtration
224 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: ATP-dependent 6-phosphofructokinase

F: ATP-dependent 6-phosphofructokinase

G: ATP-dependent 6-phosphofructokinase

H: ATP-dependent 6-phosphofructokinase

hetero molecules

defined by author&software
224 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	115.251, 132.513, 282.699
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 10 - 485 / Label seq-ID: 30 - 505

NCS ensembles :

#1: Protein	ATP-dependent 6-phosphofructokinase / Phosphofructokinase / Phosphohexokinase Mass: 55764.707 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: pfk / Production host: Escherichia coli (E. coli) / References: UniProt: O15648, 6-phosphofructokinase
#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-JJ8 / 1-[(3,4-dichlorophenyl)methyl]imidazole Mass: 227.090 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₈Cl₂N₂

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.16 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / Details: 9.5% PEG, 8000, 0.1 M sodium cacodylate pH 7.4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 3.4→96.67 Å / Num. obs: 60210 / % possible obs: 99.73 % / Redundancy: 4.4 % / Net I/σ(I): 8.4
Reflection shell	Resolution: 3.4→3.522 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0241	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3f5m

3f5m

Resolution: 3.4→96.67 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.921 / SU B: 104.039 / SU ML: 0.654 / Cross valid method: THROUGHOUT / ESU R Free: 0.649 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2671	2969	4.9 %	RANDOM
R_work	0.24968	-	-	-
obs	0.25054	57240	99.77 %	-

Solvent computation

Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å

Displacement parameters

B_iso mean: 120.881 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.37 Å²	0 Å²	0 Å²
2-	-	5.64 Å²	-0 Å²
3-	-	-	-11.01 Å²

Refinement step

Cycle: LAST / Resolution: 3.4→96.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28111	0	144	0	28255

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	28714
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	27508
X-RAY DIFFRACTION	r_angle_refined_deg	1.484	1.643	38853
X-RAY DIFFRACTION	r_angle_other_deg	1.209	1.576	63465
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.996	5	3621
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.017	20.259	1542
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.304	15	4964
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.033	15	299
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	3838
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	32211
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	6184
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	14216	0.07
1	2	B	14216	0.07
2	1	A	13993	0.09
2	2	C	13993	0.09
3	1	A	14150	0.08
3	2	D	14150	0.08
4	1	A	14026	0.09
4	2	E	14026	0.09
5	1	A	14152	0.08
5	2	F	14152	0.08
6	1	A	13856	0.09
6	2	G	13856	0.09
7	1	A	14158	0.08
7	2	H	14158	0.08
8	1	B	14144	0.09
8	2	C	14144	0.09
9	1	B	14175	0.07
9	2	D	14175	0.07
10	1	B	14104	0.09
10	2	E	14104	0.09
11	1	B	14287	0.08
11	2	F	14287	0.08
12	1	B	13948	0.09
12	2	G	13948	0.09
13	1	B	14156	0.07
13	2	H	14156	0.07
14	1	C	13963	0.09
14	2	D	13963	0.09
15	1	C	13938	0.1
15	2	E	13938	0.1
16	1	C	13999	0.09
16	2	F	13999	0.09
17	1	C	13892	0.1
17	2	G	13892	0.1
18	1	C	13936	0.09
18	2	H	13936	0.09
19	1	D	14025	0.08
19	2	E	14025	0.08
20	1	D	14148	0.07
20	2	F	14148	0.07
21	1	D	13923	0.09
21	2	G	13923	0.09
22	1	D	14100	0.07
22	2	H	14100	0.07
23	1	E	14168	0.08
23	2	F	14168	0.08
24	1	E	13918	0.09
24	2	G	13918	0.09
25	1	E	13995	0.08
25	2	H	13995	0.08
26	1	F	13919	0.09
26	2	G	13919	0.09
27	1	F	14169	0.07
27	2	H	14169	0.07
28	1	G	13882	0.09
28	2	H	13882	0.09

LS refinement shell

Resolution: 3.4→3.488 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.407	216	-
R_work	0.419	4157	-
obs	-	-	99.89 %

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	3.0106	0.2734	-0.9389	1.7884	-0.3434	3.0389	0.1002	-0.1829	0.4395	-0.0498	0.0694	0.1859	-0.6599	-0.4046	-0.1696	0.1747	0.0703	-0.003	0.1257	-0.0131	0.8926	-17.418	-17.25	44.351
2	2.0074	0.4268	0.2912	2.6439	0.3889	2.1537	-0.0457	-0.704	-0.0373	0.4005	0.1663	-0.3182	-0.0064	0.3283	-0.1206	0.0854	0.0373	-0.0204	0.3814	-0.0859	1.0354	3.519	-27.096	55.709
3	2.7926	0.1231	0.0244	1.6944	0.2631	2.2391	0.0042	0.3289	-0.6423	-0.4758	-0.0087	-0.2432	0.5065	0.4599	0.0045	0.4287	0.0263	0.0576	0.2204	-0.1569	1.1378	7.028	-49.147	24.301
4	1.9904	-0.4601	-0.3597	1.1882	0.2287	2.1025	0.2915	0.9408	0.191	-0.8588	-0.0956	-0.0071	-0.2996	-0.0211	-0.1959	0.6593	0.0095	0.0963	0.4996	-0.0242	0.9399	-1.994	-28.885	11.192
5	3.0336	1.0256	0.4027	2.3136	0.4617	2.4572	-0.1523	0.029	-0.5991	-0.0103	0.1131	-0.5352	0.6213	0.2885	0.0392	0.2193	0.0309	0.12	0.081	-0.0566	1.3011	-39.338	19.797	50.277
6	2.8086	1.2402	-0.2837	3.1038	-0.305	2.1049	0.0288	-0.5393	0.1571	0.4357	-0.2134	0.1813	-0.06	-0.2908	0.1846	0.0966	-0.0137	0.0747	0.1725	-0.1237	1.0184	-60.698	30.877	59.658
7	1.6035	0.1589	-0.3437	1.9206	-0.3868	1.5859	-0.1656	0.8186	0.5125	-0.8587	0.1559	0.2812	-0.324	-0.5002	0.0097	0.7628	-0.148	-0.1707	0.5931	0.1839	1.4955	-63.805	48.492	25.795
8	1.1085	-0.1396	0.1466	0.7922	0.0377	1.806	-0.1527	0.9975	0.0516	-0.9071	0.0609	-0.1017	0.2322	-0.1089	0.0918	1.1857	-0.4061	0.1209	0.9958	-0.1391	1.3679	-54.36	27.117	15.435

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 485
2	X-RAY DIFFRACTION	2	B	10 - 485
3	X-RAY DIFFRACTION	3	C	10 - 485
4	X-RAY DIFFRACTION	4	D	10 - 485
5	X-RAY DIFFRACTION	5	E	10 - 485
6	X-RAY DIFFRACTION	6	F	10 - 485
7	X-RAY DIFFRACTION	7	G	10 - 485
8	X-RAY DIFFRACTION	8	H	10 - 485

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