4E00 | pdb_00004e00

Crystal structure of branched-chain alpha-ketoacid dehydrogenase kinase/3,6-dichlorobenzo[b]thiophene-2-carboxylic acid complex with ADP

PDB DOI: https://doi.org/10.2210/pdb4E00/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Rattus norvegicus
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2012-03-01 Released: 2013-03-27
Deposition Author(s): Tso, S.C., Chuang, J.L., Gui, W.J., Wynn, R.M., Li, J., Chuang, D.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.234 (Depositor), 0.225 (DCC)
R-Value Work:
0.207 (Depositor), 0.204 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of branched-chain alpha-ketoacid dehydrogenase kinase/3,6-dichlorobenzo[b]thiophene-2-carboxylic acid complex with ADP

Tso, S.C., Chuang, J.L., Gui, W.J., Wynn, R.M., Li, J., Chuang, D.T.

To be published.

Macromolecule Content

Total Structure Weight: 48.11 kDa
Atom Count: 2,607
Modeled Residue Count: 308
Deposited Residue Count: 418
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial	A	418	Rattus norvegicus	Mutation(s): 0 Gene Names: Bckdk EC: 2.7.11.4 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt
Find proteins for Q00972 (Rattus norvegicus) Explore Q00972 Go to UniProtKB: Q00972
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00972
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
0F1 Query on 0F1 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	3,6-dichloro-1-benzothiophene-2-carboxylic acid C₉ H₄ Cl₂ O₂ S AAHPIJMQJAZYTM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.234 (Depositor), 0.225 (DCC)
R-Value Work: 0.207 (Depositor), 0.204 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.057	α = 90
b = 128.057	β = 90
c = 73.775	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-03-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-03-27
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.