[English] 日本語
Yorodumi
- PDB-6lin: Crystal structure of human PDK2 complexed with GM10030 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lin
TitleCrystal structure of human PDK2 complexed with GM10030
Components[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
KeywordsTRANSFERASE / mitochondria / kinase / inhibitor
Function / homology
Function and homology information


[pyruvate dehydrogenase (acetyl-transferring)] kinase / pyruvate dehydrogenase (acetyl-transferring) kinase activity / regulation of pyruvate decarboxylation to acetyl-CoA / Regulation of pyruvate dehydrogenase (PDH) complex / regulation of ketone metabolic process / pyruvate dehydrogenase complex / regulation of pH / cellular response to nutrient / Signaling by Retinoic Acid / regulation of gluconeogenesis ...[pyruvate dehydrogenase (acetyl-transferring)] kinase / pyruvate dehydrogenase (acetyl-transferring) kinase activity / regulation of pyruvate decarboxylation to acetyl-CoA / Regulation of pyruvate dehydrogenase (PDH) complex / regulation of ketone metabolic process / pyruvate dehydrogenase complex / regulation of pH / cellular response to nutrient / Signaling by Retinoic Acid / regulation of gluconeogenesis / intrinsic apoptotic signaling pathway by p53 class mediator / regulation of glucose metabolic process / regulation of calcium-mediated signaling / cellular response to reactive oxygen species / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / protein kinase activity / mitochondrial matrix / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal / Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain superfamily / PDK/BCKDK protein kinase / Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Chem-EH0 / DI(HYDROXYETHYL)ETHER / [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsKang, J. / Kim, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2016R1D1A1B03930716 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural basis for the inhibition of PDK2 by novel ATP- and lipoyl-binding site targeting compounds.
Authors: Kang, J. / Pagire, H.S. / Kang, D. / Song, Y.H. / Lee, I.K. / Lee, K.T. / Park, C.J. / Ahn, J.H. / Kim, J.
History
DepositionDec 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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 visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
B: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
C: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
D: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,14512
Polymers185,3434
Non-polymers2,8028
Water2,702150
1
A: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
B: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1617
Polymers92,6712
Non-polymers1,4905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-40 kcal/mol
Surface area32980 Å2
MethodPISA
2
C: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
D: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9835
Polymers92,6712
Non-polymers1,3123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-11 kcal/mol
Surface area32840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.420, 156.186, 102.012
Angle α, β, γ (deg.)90.000, 103.970, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUTHRTHRAA13 - 38438 - 409
21LEULEUTHRTHRBB13 - 38438 - 409
12ASPASPTHRTHRAA4 - 38429 - 409
22ASPASPTHRTHRCC4 - 38429 - 409
13LEULEUHISHISAA13 - 38138 - 406
23LEULEUHISHISDD13 - 38138 - 406
14LEULEUGLNGLNBB13 - 38338 - 408
24LEULEUGLNGLNCC13 - 38338 - 408
15LEULEUTYRTYRBB13 - 38238 - 407
25LEULEUTYRTYRDD13 - 38238 - 407
16LEULEUHISHISCC13 - 38138 - 406
26LEULEUHISHISDD13 - 38138 - 406

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial / Pyruvate dehydrogenase kinase 2 / Pyruvate dehydrogenase kinase isoform 2 / PDKII


Mass: 46335.676 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDK2, PDHK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q15119, [pyruvate dehydrogenase (acetyl-transferring)] kinase

-
Non-polymers , 5 types, 158 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical
ChemComp-EH0 / 4-[[[4-[3,5-bis(fluoranyl)-4-(4-oxidanyl-4-oxidanylidene-butoxy)phenyl]-5-[5-chloranyl-2,4-bis(oxidanyl)phenyl]-1,2-oxazol-3-yl]carbonylamino]methyl]benzoic acid


Mass: 602.924 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C28H21ClF2N2O9 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris pH 6.5, 25% w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. obs: 49194 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.104 / Rrim(I) all: 0.245 / Χ2: 1.851 / Net I/σ(I): 4.7 / Num. measured all: 259808
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.67-2.725.21.39924700.4120.6541.5482.33299.7
2.72-2.775.31.70624280.6280.7971.8881.5699.8
2.77-2.825.21.35724590.6730.6391.5041.52199.9
2.82-2.885.31.11824560.780.5231.2381.55899.8
2.88-2.945.31.00724520.7870.4711.1141.59699.9
2.94-3.015.30.89324600.8140.4170.9891.59499.9
3.01-3.085.40.78424360.8640.3630.8671.58699.9
3.08-3.175.30.62224740.8690.290.6881.635100
3.17-3.265.40.48324170.9120.2240.5341.681100
3.26-3.365.40.40624860.9460.1880.4491.666100
3.36-3.485.20.33324560.9510.1560.3692.21599.9
3.48-3.625.40.29624520.970.1380.3271.825100
3.62-3.795.20.22124950.9750.1040.2452.436100
3.79-3.995.20.17524330.9820.0840.1952.437100
3.99-4.245.40.13424320.990.0630.1491.83599.8
4.24-4.565.30.09924690.9930.0470.111.984100
4.56-5.025.40.08724750.9950.0410.0971.842100
5.02-5.755.40.09224910.9940.0430.1011.69299.9
5.75-7.245.30.09824820.9930.0460.1081.7499.9
7.24-5050.06224710.9960.0310.072.3698.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MP2

4mp2


Resolution: 2.67→39.08 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.887 / SU B: 17.655 / SU ML: 0.355 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2797 2442 5 %RANDOM
Rwork0.2232 ---
obs0.2261 46026 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.03 Å2 / Biso mean: 48.125 Å2 / Biso min: 17.01 Å2
Baniso -1Baniso -2Baniso -3
1-3.65 Å20 Å22.11 Å2
2---0.78 Å20 Å2
3----3.48 Å2
Refinement stepCycle: final / Resolution: 2.67→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11286 0 191 150 11627
Biso mean--62.45 37.73 -
Num. residues----1448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01311763
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710522
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.66115986
X-RAY DIFFRACTIONr_angle_other_deg1.2411.5724377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17951442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.07522.402562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.525151895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5571560
X-RAY DIFFRACTIONr_chiral_restr0.0680.21521
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022408
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A107180.11
12B107180.11
21A109340.09
22C109340.09
31A106330.11
32D106330.11
41B107540.1
42C107540.1
51B112050.07
52D112050.07
61C106990.1
62D106990.1
LS refinement shellResolution: 2.67→2.739 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 163 -
Rwork0.321 3392 -
all-3555 -
obs--99.69 %

+
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