5RVX | pdb_00005rvx

PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z804566442

PDB DOI: https://doi.org/10.2210/pdb5RVX/pdb
Deposition Group: G_1002178 (changed state) ExploreG_1002178

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-10-27 Released: 2020-11-25
Deposition Author(s): Bezerra, G.A., Foster, W.R., Bailey, H.J., Shrestha, L., Krojer, T., Brandao-Neto, J., Douangamath, A., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Yue, W.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.198 (Depositor), 0.210 (DCC)
R-Value Work:
0.171 (Depositor), 0.180 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

PanDDA analysis group deposition

Bezerra, G.A., Foster, W.R., Bailey, H.J., Shrestha, L., Krojer, T., Brandao-Neto, J., Douangamath, A., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Yue, W.W.

To be published.

Macromolecule Content

Total Structure Weight: 203.27 kDa
Atom Count: 15,404
Modelled Residue Count: 1,734
Deposited Residue Count: 1,796
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial	A, B	898	Homo sapiens	Mutation(s): 0 Gene Names: DHTKD1, KIAA1630 EC: 1.2.4.2 (PDB Primary Data), 1.2.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96HY7 (Homo sapiens) Explore Q96HY7 Go to UniProtKB: Q96HY7
PHAROS: Q96HY7 GTEx: ENSG00000181192
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96HY7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP Query on TPP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
B0Y (Subject of Investigation/LOI) Query on B0Y Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	5-ethyl-~{N}-[(1-methylpyrazol-4-yl)methyl]thiophene-2-carboxamide C₁₂ H₁₅ N₃ O S IMEUOMKMOTYOQB-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	E [auth A], F [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B]