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

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Basic information

Entry
Database: PDB / ID: 6qu5
TitleCrystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an allosteric inhibitor ctcb12
ComponentsATP-dependent 6-phosphofructokinase
KeywordsTRANSFERASE / 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
Pyrophosphate-dependent phosphofructokinase TP0108-type / : / Phosphofructokinase domain / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 1-[(3,4-dichlorophenyl)methyl]imidazole / ATP-dependent 6-phosphofructokinase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsMcNae, I.W. / Dornan, J. / Walkinshaw, M.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: 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. ...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.A. / Highton, A.J. / Keats, A.J. / Vong, A. / Dornan, J. / Mottram, J.C. / Michels, P.A.M. / Pettit, S. / Walkinshaw, M.D.
History
DepositionFeb 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Mar 3, 2021Group: 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 1.3Jan 24, 2024Group: 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
Revision 1.4Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)448,29320
Polymers446,1188
Non-polymers2,17512
Water00
1
A: ATP-dependent 6-phosphofructokinase
B: ATP-dependent 6-phosphofructokinase
C: ATP-dependent 6-phosphofructokinase
D: ATP-dependent 6-phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,46612
Polymers223,0594
Non-polymers1,4078
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21160 Å2
ΔGint-66 kcal/mol
Surface area69440 Å2
MethodPISA
2
E: ATP-dependent 6-phosphofructokinase
F: ATP-dependent 6-phosphofructokinase
G: ATP-dependent 6-phosphofructokinase
H: ATP-dependent 6-phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,8278
Polymers223,0594
Non-polymers7684
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20240 Å2
ΔGint-59 kcal/mol
Surface area70470 Å2
MethodPISA
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 number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

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

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18BB
28CC
19BB
29DD
110BB
210EE
111BB
211FF
112BB
212GG
113BB
213HH
114CC
214DD
115CC
215EE
116CC
216FF
117CC
217GG
118CC
218HH
119DD
219EE
120DD
220FF
121DD
221GG
122DD
222HH
123EE
223FF
124EE
224GG
125EE
225HH
126FF
226GG
127FF
227HH
128GG
228HH

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#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
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 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

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

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Processing

Software
NameVersionClassification
REFMAC5.8.0241refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3f5m

3f5m


Resolution: 3.4→96.67 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 2969 4.9 %RANDOM
Rwork0.24968 ---
obs0.25054 57240 99.77 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 120.881 Å2
Baniso -1Baniso -2Baniso -3
1-5.37 Å20 Å20 Å2
2--5.64 Å2-0 Å2
3----11.01 Å2
Refinement stepCycle: LAST / Resolution: 3.4→96.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28111 0 144 0 28255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01328714
X-RAY DIFFRACTIONr_bond_other_d0.0010.01727508
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.64338853
X-RAY DIFFRACTIONr_angle_other_deg1.2091.57663465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99653621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.01720.2591542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.304154964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.03315299
X-RAY DIFFRACTIONr_chiral_restr0.0650.23838
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0232211
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026184
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A142160.07
12B142160.07
21A139930.09
22C139930.09
31A141500.08
32D141500.08
41A140260.09
42E140260.09
51A141520.08
52F141520.08
61A138560.09
62G138560.09
71A141580.08
72H141580.08
81B141440.09
82C141440.09
91B141750.07
92D141750.07
101B141040.09
102E141040.09
111B142870.08
112F142870.08
121B139480.09
122G139480.09
131B141560.07
132H141560.07
141C139630.09
142D139630.09
151C139380.1
152E139380.1
161C139990.09
162F139990.09
171C138920.1
172G138920.1
181C139360.09
182H139360.09
191D140250.08
192E140250.08
201D141480.07
202F141480.07
211D139230.09
212G139230.09
221D141000.07
222H141000.07
231E141680.08
232F141680.08
241E139180.09
242G139180.09
251E139950.08
252H139950.08
261F139190.09
262G139190.09
271F141690.07
272H141690.07
281G138820.09
282H138820.09
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 216 -
Rwork0.419 4157 -
obs--99.89 %
Refinement TLS params.

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

IDL11 (°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)
13.01060.2734-0.93891.7884-0.34343.03890.1002-0.18290.4395-0.04980.06940.1859-0.6599-0.4046-0.16960.17470.0703-0.0030.1257-0.01310.8926-17.418-17.2544.351
22.00740.42680.29122.64390.38892.1537-0.0457-0.704-0.03730.40050.1663-0.3182-0.00640.3283-0.12060.08540.0373-0.02040.3814-0.08591.03543.519-27.09655.709
32.79260.12310.02441.69440.26312.23910.00420.3289-0.6423-0.4758-0.0087-0.24320.50650.45990.00450.42870.02630.05760.2204-0.15691.13787.028-49.14724.301
41.9904-0.4601-0.35971.18820.22872.10250.29150.94080.191-0.8588-0.0956-0.0071-0.2996-0.0211-0.19590.65930.00950.09630.4996-0.02420.9399-1.994-28.88511.192
53.03361.02560.40272.31360.46172.4572-0.15230.029-0.5991-0.01030.1131-0.53520.62130.28850.03920.21930.03090.120.081-0.05661.3011-39.33819.79750.277
62.80861.2402-0.28373.1038-0.3052.10490.0288-0.53930.15710.4357-0.21340.1813-0.06-0.29080.18460.0966-0.01370.07470.1725-0.12371.0184-60.69830.87759.658
71.60350.1589-0.34371.9206-0.38681.5859-0.16560.81860.5125-0.85870.15590.2812-0.324-0.50020.00970.7628-0.148-0.17070.59310.18391.4955-63.80548.49225.795
81.1085-0.13960.14660.79220.03771.806-0.15270.99750.0516-0.90710.0609-0.10170.2322-0.10890.09181.1857-0.40610.12090.9958-0.13911.3679-54.3627.11715.435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 485
2X-RAY DIFFRACTION2B10 - 485
3X-RAY DIFFRACTION3C10 - 485
4X-RAY DIFFRACTION4D10 - 485
5X-RAY DIFFRACTION5E10 - 485
6X-RAY DIFFRACTION6F10 - 485
7X-RAY DIFFRACTION7G10 - 485
8X-RAY DIFFRACTION8H10 - 485

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