8F4Q

rat branched chain ketoacid dehydrogenase kinase in complex with inhibtors

PDB DOI: https://doi.org/10.2210/pdb8F4Q/pdb

Classification: SIGNALING PROTEIN,TRANSFERASE/INHIBITOR
Organism(s): Rattus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-11-11 Released: 2023-12-13
Deposition Author(s): Liu, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.271
R-Value Work: 0.234
R-Value Observed: 0.235

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Discovery of branched-chain ketoacid dehydrogenase kinase (BDK) inhibitors acting as stabilizers or destabilizers

Roth Flach, R., Filipski, K., Bollinger, E.

To be published.

Macromolecule Content

Total Structure Weight: 45.59 kDa
Atom Count: 2,700
Modelled Residue Count: 319
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial	A	388	Rattus	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q00972
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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]
XER (Subject of Investigation/LOI) Query on XER Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	3-chloro-5-fluorothieno[3,2-b]thiophene-2-carboxylic acid C₇ H₂ Cl F O₂ S₂ UXMBSHHPPVOPJU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]