5RVW | pdb_00005rvw

PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z1587220559

• PDB DOI: https://doi.org/10.2210/pdb5RVW/pdb
• Deposition Group: G_1002178 (changed state) | Explore  G_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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.189 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 203.02 kDa 
• Atom Count: 15,390 
• Modeled Residue Count: 1,734 
• Deposited Residue Count: 1,796 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP	C [auth A], F [auth B]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
T1J (Subject of Investigation/LOI)	E [auth B]	2-{[(1H-benzimidazol-2-yl)amino]methyl}phenol C14 H13 N3 O OCDMDLRMBVJKCG-UHFFFAOYSA-N
MG	D [auth A], G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.189 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.074	α = 90
b = 147.025	β = 102.7
c = 87.377	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 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.

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2026-02-18
  Changes: Refinement description, Structure summary