[English] 日本語
Yorodumi
- PDB-4e01: Crystal structure of branched-chain alpha-ketoacid dehydrogenase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 40
TitleCrystal structure of branched-chain alpha-ketoacid dehydrogenase kinase/3,6-dichlorobenzo[b]thiophene-2-carboxylic acid complex with AMPPNP
Components[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / GHKL protein kinase / Allosteric kinase inhibitor / Branched-chain alpha-ketoacid / Branched-chain amino acids / Maple syrup urine disease / Diabetes and obesity / Bergerat nucleotide-binding fold / protein kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / : / Branched-chain amino acid catabolism / L-leucine catabolic process / valine catabolic process / isoleucine catabolic process / pyruvate dehydrogenase (acetyl-transferring) kinase activity / branched-chain amino acid catabolic process / lipid biosynthetic process ...[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / : / Branched-chain amino acid catabolism / L-leucine catabolic process / valine catabolic process / isoleucine catabolic process / pyruvate dehydrogenase (acetyl-transferring) kinase activity / branched-chain amino acid catabolic process / lipid biosynthetic process / protein serine/threonine phosphatase activity / regulation of glucose metabolic process / spermatogenesis / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding
Similarity search - Function
Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain / 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 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain ...Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain / 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 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3,6-dichloro-1-benzothiophene-2-carboxylic acid / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Branched-chain alpha-ketoacid dehydrogenase kinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsTso, S.C. / Chuang, J.L. / Gui, W.J. / Wynn, R.M. / Li, J. / Chuang, D.T.
CitationJournal: To be Published
Title: Structures of branched-chain alpha-ketoacid dehydrogenase kinase-inhibitor complexes
Authors: Tso, S.C. / Chuang, J.L. / Gui, W.J. / Wynn, R.M. / Li, J. / Chuang, D.T.
History
DepositionMar 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1915
Polymers47,3741
Non-polymers8174
Water2,126118
1
A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules

A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,38210
Polymers94,7482
Non-polymers1,6338
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3790 Å2
ΔGint-34 kcal/mol
Surface area29000 Å2
MethodPISA
2
A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules

A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules

A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules

A: [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,76420
Polymers189,4974
Non-polymers3,26716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area11320 Å2
ΔGint-70 kcal/mol
Surface area54260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.277, 127.277, 73.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial / Branched-chain alpha-ketoacid dehydrogenase kinase / BCKD-kinase / BCKDHKIN


Mass: 47374.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Bckdk / Plasmid: pTrckHisB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21GroESL
References: UniProt: Q00972, [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase

-
Non-polymers , 5 types, 122 molecules

#2: Chemical ChemComp-0F1 / 3,6-dichloro-1-benzothiophene-2-carboxylic acid


Mass: 247.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H4Cl2O2S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14% peg8000, 0.1 M Tris, pH8.5, 1.2 M NaCl, 125mM KCl, 150mM Arg-HCl, 20mM MgCl2, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2011 / Details: mirrors
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. all: 43957 / Num. obs: 43789 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Biso Wilson estimate: 40.5 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.071 / Net I/σ(I): 20.5
Reflection shellResolution: 1.97→2 Å / Redundancy: 8 % / Rmerge(I) obs: 0.937 / Mean I/σ(I) obs: 2.08 / Num. unique all: 2098 / Rsym value: 0.854 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.refine: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→40.249 Å / SU ML: 0.52 / σ(F): 1.35 / Phase error: 20.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 2000 4.57 %random
Rwork0.1974 ---
obs0.1984 41745 99.5 %-
all-43743 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.758 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.7609 Å20 Å2-0 Å2
2---3.7609 Å2-0 Å2
3---7.5218 Å2
Refinement stepCycle: LAST / Resolution: 1.97→40.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 47 118 2643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072590
X-RAY DIFFRACTIONf_angle_d1.1113512
X-RAY DIFFRACTIONf_dihedral_angle_d19.489999
X-RAY DIFFRACTIONf_chiral_restr0.066388
X-RAY DIFFRACTIONf_plane_restr0.005446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9626-2.01160.32221360.29042834X-RAY DIFFRACTION96
2.0116-2.0660.24451400.22542920X-RAY DIFFRACTION99
2.066-2.12680.24941410.20772943X-RAY DIFFRACTION100
2.1268-2.19550.21271420.18892962X-RAY DIFFRACTION100
2.1955-2.27390.20141400.18732929X-RAY DIFFRACTION100
2.2739-2.3650.25881410.18892956X-RAY DIFFRACTION100
2.365-2.47260.21981430.19792980X-RAY DIFFRACTION100
2.4726-2.60290.1971420.19882967X-RAY DIFFRACTION100
2.6029-2.7660.21141430.19752977X-RAY DIFFRACTION100
2.766-2.97950.23351440.21043000X-RAY DIFFRACTION100
2.9795-3.27920.23451440.20163010X-RAY DIFFRACTION100
3.2792-3.75340.20161460.19683033X-RAY DIFFRACTION100
3.7534-4.72770.19381450.17453055X-RAY DIFFRACTION100
4.7277-40.2570.24221530.20623177X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 3.0283 Å / Origin y: -30.2429 Å / Origin z: 9.655 Å
111213212223313233
T0.2432 Å20.0058 Å2-0.0014 Å2-0.2545 Å20.0475 Å2--0.2525 Å2
L3.4562 °20.6908 °2-0.88 °2-1.3746 °2-0.4672 °2--0.773 °2
S-0.0363 Å °-0.3973 Å °-0.1477 Å °0.0056 Å °0.0043 Å °0.2185 Å °0.0642 Å °-0.0028 Å °0.0262 Å °
Refinement TLS groupSelection details: all

+
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