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- PDB-6nu1: Crystal Structure of Human PKM2 in Complex with L-cysteine -

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Basic information

Entry
Database: PDB / ID: 6nu1
TitleCrystal Structure of Human PKM2 in Complex with L-cysteine
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / PYRUVATE KINASE M2 / CYSTEINE / INHIBITION / GLYCOLYSIS
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 ...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 / glycolytic process / non-specific protein-tyrosine kinase / cilium / cellular response to insulin stimulus / extracellular vesicle / MHC class II protein complex binding / collagen-containing extracellular matrix / protein tyrosine kinase activity / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / transcription coactivator activity / non-specific serine/threonine protein kinase / cadherin binding / phosphorylation / mRNA binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
CYSTEINE / 1,6-di-O-phosphono-beta-D-fructofuranose / : / OXALATE ION / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSrivastava, D. / Nandi, S. / Dey, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CLP 1506181 United States
CitationJournal: Biochemistry / Year: 2019
Title: Mechanistic and Structural Insights into Cysteine-Mediated Inhibition of Pyruvate Kinase Muscle Isoform 2.
Authors: Srivastava, D. / Nandi, S. / Dey, M.
History
DepositionJan 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / 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_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_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.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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate kinase PKM
B: Pyruvate kinase PKM
C: Pyruvate kinase PKM
D: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,12622
Polymers240,7534
Non-polymers2,37318
Water11,097616
1
D: Pyruvate kinase PKM
hetero molecules

A: Pyruvate kinase PKM
hetero molecules

B: Pyruvate kinase PKM
hetero molecules

C: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,12622
Polymers240,7534
Non-polymers2,37318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_656x+1,y,z+11
crystal symmetry operation2_746-x+2,y-1/2,-z+11
Buried area19640 Å2
ΔGint-145 kcal/mol
Surface area67100 Å2
MethodPISA
2
D: Pyruvate kinase PKM
hetero molecules

A: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,56311
Polymers120,3772
Non-polymers1,1869
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area7650 Å2
ΔGint-59 kcal/mol
Surface area36330 Å2
MethodPISA
3
B: Pyruvate kinase PKM
hetero molecules

A: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,56311
Polymers120,3772
Non-polymers1,1869
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4410 Å2
ΔGint-38 kcal/mol
Surface area37620 Å2
MethodPISA
4
B: Pyruvate kinase PKM
hetero molecules

C: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,56311
Polymers120,3772
Non-polymers1,1869
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area7670 Å2
ΔGint-61 kcal/mol
Surface area35090 Å2
MethodPISA
5
D: Pyruvate kinase PKM
hetero molecules

C: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,56311
Polymers120,3772
Non-polymers1,1869
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_746-x+2,y-1/2,-z+11
Buried area4420 Å2
ΔGint-35 kcal/mol
Surface area40280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.829, 155.918, 94.136
Angle α, β, γ (deg.)90.00, 103.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Pyruvate kinase PKM / Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate ...Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate kinase 2/3 / Pyruvate kinase muscle isozyme / Thyroid hormone-binding protein 1 / THBP1 / Tumor M2-PK / p58


Mass: 60188.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKM, OIP3, PK2, PK3, PKM2 / Production host: Escherichia coli (E. coli) / 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
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 630 molecules

#2: Chemical
ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M SODIUM THIOCYANATE, 100 mM BIS-TRIS PROPANE, 16-20% PEG 3350, 0.2 M NDSB-221
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.25→24.7 Å / Num. obs: 106086 / % possible obs: 97.7 % / Redundancy: 3.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.067 / Rrim(I) all: 0.127 / Net I/σ(I): 10.2
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 15672 / CC1/2: 0.768 / Rpim(I) all: 0.319 / Rrim(I) all: 0.619 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B2D, 3SRH

4b2d

3srh


Resolution: 2.25→24.7 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.55
RfactorNum. reflection% reflection
Rfree0.2352 5285 4.98 %
Rwork0.1908 --
obs0.193 106046 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→24.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14322 0 138 616 15076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314696
X-RAY DIFFRACTIONf_angle_d0.60219960
X-RAY DIFFRACTIONf_dihedral_angle_d14.7668925
X-RAY DIFFRACTIONf_chiral_restr0.0462354
X-RAY DIFFRACTIONf_plane_restr0.0032597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.27560.34211500.24933462X-RAY DIFFRACTION99
2.2756-2.30230.28981680.23293371X-RAY DIFFRACTION99
2.3023-2.33040.28661740.22783396X-RAY DIFFRACTION99
2.3304-2.35980.27781780.22983409X-RAY DIFFRACTION99
2.3598-2.39090.29841780.23083386X-RAY DIFFRACTION99
2.3909-2.42360.27541720.2263413X-RAY DIFFRACTION99
2.4236-2.45820.28151830.22253374X-RAY DIFFRACTION99
2.4582-2.49480.30441870.22523394X-RAY DIFFRACTION99
2.4948-2.53380.29121900.22443364X-RAY DIFFRACTION99
2.5338-2.57530.30211730.21823386X-RAY DIFFRACTION99
2.5753-2.61960.27851760.21843419X-RAY DIFFRACTION99
2.6196-2.66720.23881790.21013389X-RAY DIFFRACTION98
2.6672-2.71850.27571620.20663370X-RAY DIFFRACTION99
2.7185-2.77390.25821990.20173365X-RAY DIFFRACTION98
2.7739-2.83410.23751980.19663369X-RAY DIFFRACTION99
2.8341-2.89990.2641810.20133363X-RAY DIFFRACTION99
2.8999-2.97230.24971970.19643373X-RAY DIFFRACTION99
2.9723-3.05260.23961600.19093395X-RAY DIFFRACTION98
3.0526-3.14220.2371800.19233394X-RAY DIFFRACTION98
3.1422-3.24340.24271530.19173369X-RAY DIFFRACTION98
3.2434-3.35910.23641860.1983356X-RAY DIFFRACTION98
3.3591-3.49320.26171560.19013326X-RAY DIFFRACTION97
3.4932-3.65170.23491670.17873352X-RAY DIFFRACTION96
3.6517-3.84360.22571630.17243275X-RAY DIFFRACTION96
3.8436-4.08340.211800.17043303X-RAY DIFFRACTION95
4.0834-4.3970.19961730.16473274X-RAY DIFFRACTION96
4.397-4.83650.18781830.15223252X-RAY DIFFRACTION94
4.8365-5.52950.18581840.17543300X-RAY DIFFRACTION95
5.5295-6.94090.26031850.20353263X-RAY DIFFRACTION95
6.9409-24.70370.18521700.17983299X-RAY DIFFRACTION94

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