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)

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
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55809
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth C]	E [auth A], F [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth C]

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

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Entry History

Deposition Data

Released Date: 2008-08-12

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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