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- PDB-3pp7: Crystal structure of Leishmania mexicana pyruvate kinase in compl... -

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Basic information

Entry
Database: PDB / ID: 3pp7
TitleCrystal structure of Leishmania mexicana pyruvate kinase in complex with the drug suramin, an inhibitor of glycolysis.
ComponentsPyruvate kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TIM Barrel / Glycolysis / ADP/ATP binding / Cytosol / symmetric drug / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / kinase activity / phosphorylation / magnesium ion binding / ATP binding
Similarity search - Function
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / pyrene-1,3,6,8-tetrasulfonic acid / Chem-SVR / Pyruvate kinase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMorgan, H.P. / Auld, D.S. / McNae, I.W. / Nowicki, M.W. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The trypanocidal drug suramin and other trypan blue mimetics are inhibitors of pyruvate kinases and bind to the adenosine site.
Authors: Morgan, H.P. / McNae, I.W. / Nowicki, M.W. / Zhong, W. / Michels, P.A. / Auld, D.S. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
History
DepositionNov 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Sep 21, 2011Group: Database references
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,83410
Polymers108,6732
Non-polymers2,1608
Water7,855436
1
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules

A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,66820
Polymers217,3474
Non-polymers4,32116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Unit cell
Length a, b, c (Å)123.770, 129.480, 165.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pyruvate kinase / / PK


Mass: 54336.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Strain: BEL46 / Gene: PYK / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: Q27686, pyruvate kinase

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Non-polymers , 5 types, 444 molecules

#2: Chemical ChemComp-PTK / pyrene-1,3,6,8-tetrasulfonic acid / 1,3,6,8-pyrenetetrasulfonic acid


Mass: 522.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H10O12S4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-SVR / 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID / SURAMIN / Suramin


Mass: 1297.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H40N6O23S6 / Comment: medication*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 7.2
Details: 7 12 % PEG 8,000, 20 mM triethanolamine-HCl buffer (pH 7.2), 50 mM MgCl2, 100 mM KCl and 10% glycerol, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→49.57 Å / Num. obs: 54542 / % possible obs: 98 % / Observed criterion σ(F): 2.35 / Observed criterion σ(I): 2.35 / Redundancy: 6.5 % / Biso Wilson estimate: 44.2 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.024 / Net I/σ(I): 22
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 4.5 / Num. unique all: 7772 / Rsym value: 0.146 / % possible all: 98

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PKL

1pkl


Resolution: 2.35→44.73 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 13.328 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23119 2761 5.1 %RANDOM
Rwork0.19144 ---
obs0.19342 51776 98.01 %-
all-54537 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 70.735 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.35→44.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7519 0 89 436 8044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227730
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1241.96610484
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4435984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59524.751341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.684151325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.91548
X-RAY DIFFRACTIONr_chiral_restr0.0780.21209
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215806
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4391.54895
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84827910
X-RAY DIFFRACTIONr_scbond_it1.23532835
X-RAY DIFFRACTIONr_scangle_it2.1454.52574
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 785 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.020.05
tight thermal0.040.5
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 192 -
Rwork0.222 3710 -
obs--96.56 %
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)
11.07720.1791-0.32650.5984-0.24091.2744-0.0245-0.0318-0.1248-0.01780.0073-0.2260.07830.28110.01720.10550.0225-0.01630.1817-0.05320.202740.952231.95672.4569
23.279-0.05283.03874.34450.66878.78040.1706-0.03490.16870.2831-0.1392-0.1938-0.01680.0649-0.03140.2123-0.10560.01310.0982-0.07180.122939.612960.692626.7778
30.93520.2012-0.36061.10540.02241.59140.04020.03710.1412-0.04560.0288-0.1289-0.3010.1811-0.0690.1791-0.0501-0.00460.1234-0.0260.199732.276648.19414.6159
41.00210.1344-0.01360.6324-0.00111.7114-0.0451-0.0007-0.031-0.0230.0497-0.06760.0428-0.0085-0.00450.16920.005-0.00880.1437-0.01930.208726.560230.12670.9733
52.0565-0.0304-0.37630.77010.03271.2258-0.02330.4533-0.1277-0.21510.12450.02050.1596-0.0334-0.10110.1708-0.0164-0.00160.1975-0.04690.14129.132327.6725-17.5805
60.74690.1555-0.22780.3648-0.03831.66280.025-0.1727-0.00590.14520.0349-0.0827-0.04-0.0044-0.05990.19140.0196-0.05960.18010.01060.169715.778429.542737.7618
78.23752.9987-4.71661.2275-1.71922.7881-0.5282-1.128-1.6243-0.2271-0.3888-1.03230.49781.00770.9171.3070.7476-0.00281.65950.06111.78538.42080.456430.0609
80.9503-0.02680.00180.7826-0.19341.48480.0169-0.1378-0.14560.05420.0386-0.05180.2060.0316-0.05550.19780.0115-0.05140.12740.02770.167817.312820.918528.2654
92.2443-0.250.46111.2781-0.02112.58970.0273-0.1443-0.11570.0080.06040.10850.1853-0.2013-0.08780.1564-0.0047-0.02840.18060.0340.1855-2.26127.969526.5127
104.2766-0.17520.42380.21290.09456.2131-0.1619-0.5688-0.04290.16020.19680.15540.0696-0.8453-0.03480.17730.1670.05230.37140.07640.2187-10.204635.706531.2956
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 86
2X-RAY DIFFRACTION2A87 - 187
3X-RAY DIFFRACTION3A188 - 298
4X-RAY DIFFRACTION4A299 - 424
5X-RAY DIFFRACTION5A425 - 498
6X-RAY DIFFRACTION6B1 - 86
7X-RAY DIFFRACTION7B87 - 189
8X-RAY DIFFRACTION8B190 - 367
9X-RAY DIFFRACTION9B368 - 445
10X-RAY DIFFRACTION10B446 - 498

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