3DLX | pdb_00003dlx

Crystal structure of human 3-oxoacid CoA transferase 1

• PDB DOI: https://doi.org/10.2210/pdb3DLX/pdb

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


• Deposited: 2008-06-30 Released: 2008-08-12 
• Deposition Author(s): Kavanagh, K.L., Shafqat, N., Yue, W.W., Picaud, S., Murray, J.W., Maclean, E.M., von Delft, F., Roos, A.K., Arrowsmith, C.H., Wikstrom, M., Edwards, A.M., Bountra, C., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.225 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human 3-oxoacid CoA transferase 1.

Kavanagh, K.L., Shafqat, N., Yue, W.W., Picaud, S., Murray, J.W., Maclean, E.M., von Delft, F., Roos, A.K., Arrowsmith, C.H., Wikstrom, M., Edwards, A.M., Bountra, C., Oppermann, U.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 212.79 kDa 
• Atom Count: 14,234 
• Modeled Residue Count: 1,861 
• Deposited Residue Count: 1,956 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinyl-CoA:3-ketoacid-coenzyme A transferase 1	A, B, C, D	489	Homo sapiens	Mutation(s): 0  Gene Names: OXCT1, OXCT, SCOT EC: 2.8.3.5
UniProt & NIH Common Fund Data Resources
Find proteins for P55809 (Homo sapiens) Explore P55809  Go to UniProtKB:  P55809
PHAROS:  P55809 GTEx:  ENSG00000083720

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.225 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.956	α = 90
b = 168.492	β = 105.86
c = 95.322	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Kavanagh, K.L., Shafqat, N., Yue, W.W., Picaud, S., Murray, J.W., Maclean, E.M., von Delft, F., Roos, A.K., Arrowsmith, C.H., Wikstrom, M., Edwards, A.M., Bountra, C., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description