[English] 日本語
Yorodumi
- PDB-4ip7: Structure of the S12D variant of human liver pyruvate kinase in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ip7
TitleStructure of the S12D variant of human liver pyruvate kinase in complex with citrate and FBP.
ComponentsPyruvate kinase isozymes L
KeywordsTRANSFERASE / kinase / glycolysis / allosteric / phosphorylation mimic / liver
Function / homology
Function and homology information


pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / monosaccharide binding / Glycolysis / response to metal ion ...pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / monosaccharide binding / Glycolysis / response to metal ion / response to ATP / potassium ion binding / Regulation of gene expression in beta cells / response to cAMP / response to glucose / response to nutrient / cellular response to epinephrine stimulus / glycolytic process / cellular response to insulin stimulus / kinase activity / response to hypoxia / magnesium ion binding / extracellular exosome / ATP binding / cytoplasm / cytosol
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
ADENOSINE / 1,6-di-O-phosphono-beta-D-fructofuranose / CITRATE ANION / : / DI(HYDROXYETHYL)ETHER / Pyruvate kinase PKLR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsHolyoak, T. / Fenton, A.W.
CitationJournal: Biochemistry / Year: 2013
Title: Energetic Coupling between an Oxidizable Cysteine and the Phosphorylatable N-Terminus of Human Liver Pyruvate Kinase.
Authors: Holyoak, T. / Zhang, B. / Deng, J. / Tang, Q. / Prasannan, C.B. / Fenton, A.W.
History
DepositionJan 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: 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 1.4Sep 20, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyruvate kinase isozymes L
B: Pyruvate kinase isozymes L
C: Pyruvate kinase isozymes L
D: Pyruvate kinase isozymes L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,31234
Polymers234,3694
Non-polymers3,94330
Water23,8521324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25420 Å2
ΔGint-130 kcal/mol
Surface area71520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.140, 205.078, 83.910
Angle α, β, γ (deg.)90.000, 92.150, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Pyruvate kinase isozymes L / Pyruvate kinase 1 / L-type pyruvate kinase / liver pyruvate kinase


Mass: 58592.176 Da / Num. of mol.: 4 / Fragment: liver isozyme / Mutation: S12D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PK1, PKL, PKLR / Production host: Escherichia coli (E. coli) / Strain (production host): FF50 / References: UniProt: P30613, pyruvate kinase
#4: 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


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

-
Non-polymers , 8 types, 1350 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1324 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 50 mM sodium citrate (pH 4.9), 26 mM MnCl2, 3-5% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 12, 2008
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 237180 / % possible obs: 97.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.069 / Χ2: 1.029 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.863.70.698226280.948193.3
1.86-1.944.10.657239881.127199.2
1.94-2.034.30.383239681.046199.3
2.03-2.134.30.26239781.08198.9
2.13-2.274.20.228237941.024198.1
2.27-2.444.30.13235950.994197.3
2.44-2.694.30.097232861.041196
2.69-3.084.30.072235430.986197.1
3.08-3.884.50.058241381.068199.3
3.88-504.90.036242620.974199.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VGB

2vgb


Resolution: 1.8→37.53 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2365 / WRfactor Rwork: 0.1949 / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8214 / SU B: 5.671 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1145 / SU Rfree: 0.1153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 11896 5 %RANDOM
Rwork0.1873 ---
obs0.1892 236781 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 213.31 Å2 / Biso mean: 41.9854 Å2 / Biso min: 16.68 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.04 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15291 0 226 1324 16841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.01916097
X-RAY DIFFRACTIONr_angle_refined_deg2.221.98321874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41552103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3423.015680
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.167152748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.78315163
X-RAY DIFFRACTIONr_chiral_restr0.1710.22543
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02112045
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 778 -
Rwork0.332 15133 -
all-15911 -
obs--89.42 %
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)
11.0562-1.4138-0.22964.96992.10352.1191-0.0804-0.009-0.17680.2705-0.12610.36370.1791-0.25130.20650.0339-0.01160.04990.0762-0.01060.081144.232-32.7115.716
219.2239-2.1238-7.27593.92162.2626.6628-0.3719-1.70230.08330.09020.4084-0.02620.34270.9976-0.03650.0470.09810.05590.5322-0.00330.143980.083-24.16618.496
31.14060.44820.12762.20531.23992.5886-0.11910.1149-0.0724-0.15630.0443-0.0772-0.11920.14020.07480.0258-0.01230.01810.0676-0.00390.030352.438-24.4199.636
45.1931-2.46851.87652.2396-0.53733.1073-0.0563-0.0898-0.248-0.13520.08260.20690.0859-0.1308-0.02630.0444-0.02030.00910.0893-0.02970.062330.422-30.959-0.777
54.9992.47551.57362.10480.6281.4372-0.07370.3255-0.101-0.1480.1524-0.2176-0.0095-0.0622-0.07870.0663-0.0250.01960.11290.01630.04128.2352.935-21.322
611.4445-0.0401-1.638311.63920.69753.12020.1205-0.68271.80890.443-0.09450.9931-0.3849-0.5944-0.0260.24680.14080.08870.641-0.1430.6665-10.66327.762-5.317
71.77091.26490.20822.07730.24571.53510.1538-0.1587-0.09470.1369-0.0281-0.04020.0661-0.242-0.12570.0349-0.0197-0.00140.10730.03370.02036.6955.409-9.917
84.4161-1.80761.55373.2552-1.97251.79680.04230.256-0.1153-0.3068-0.06320.00760.10920.0980.02090.0528-0.02920.01540.10250.00720.073816.115-17.673-14.069
90.9320.31891.19241.43862.4176.0252-0.1658-0.03250.1164-0.21850.1579-0.1618-0.49190.31910.00790.0581-0.0045-0.00010.1389-0.01850.063457.802-0.47631.616
109.1945-1.2233-5.14868.04550.864814.6168-1.1031-1.28-0.86510.85870.09580.19112.05640.90821.00720.72120.22510.34290.61320.19940.191240.901-27.83350.07
111.39550.17780.14142.26421.48542.0628-0.202-0.26490.1024-0.001-0.08860.213-0.2467-0.1960.29060.08420.0739-0.04610.1433-0.04550.045945.476-5.26533.227
121.3725-1.31910.81653.1868-1.18384.7139-0.00350.05490.2031-0.00640.0347-0.1855-0.13610.298-0.03120.16570.0337-0.02980.1193-0.05040.061850.21217.94924.602
131.49872.1292-0.28335.8387-1.6361.08170.2027-0.27730.18750.4352-0.16870.2037-0.139-0.0279-0.0340.087-0.01450.04610.1057-0.02540.076822.87132.702-4.15
1414.90778.08384.86555.86341.44637.5945-1.18034.0047-0.2553-0.92111.5908-0.17-0.53480.356-0.41050.5052-0.17240.21451.6973-0.00440.107825.01224.278-42.496
151.9481.01560.09972.40620.3110.82910.03440.0726-0.1076-0.15960.0512-0.3624-0.07140.0815-0.08560.0652-0.01620.05530.0645-0.01230.073130.32125.115-14.559
162.3234-0.06911.30233.0196-2.52974.5931-0.0526-0.18870.14590.37480.1-0.0874-0.257-0.1162-0.04750.1109-0.0222-0.01590.1159-0.00580.092538.26931.1369.203
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 130
2X-RAY DIFFRACTION2A131 - 228
3X-RAY DIFFRACTION3A232 - 411
4X-RAY DIFFRACTION4A412 - 543
5X-RAY DIFFRACTION5B25 - 146
6X-RAY DIFFRACTION6B147 - 234
7X-RAY DIFFRACTION7B235 - 411
8X-RAY DIFFRACTION8B412 - 543
9X-RAY DIFFRACTION9C26 - 128
10X-RAY DIFFRACTION10C129 - 234
11X-RAY DIFFRACTION11C235 - 411
12X-RAY DIFFRACTION12C412 - 543
13X-RAY DIFFRACTION13D21 - 125
14X-RAY DIFFRACTION14D126 - 219
15X-RAY DIFFRACTION15D220 - 411
16X-RAY DIFFRACTION16D412 - 543

+
About Yorodumi

-
News

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

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more