7PK0 | pdb_00007pk0

Bovine Glycine N-Acyltransferase complexed with Benzoyl-CoA

PDB DOI: https://doi.org/10.2210/pdb7PK0/pdb

Classification: TRANSFERASE
Organism(s): Bos taurus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-08-25 Released: 2022-09-07
Deposition Author(s): Opperman, D.J., Ebrecht, A.C., Read, R.J.
Funding Organization(s): Global Challenges Research Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.211 (Depositor), 0.217 (DCC)
R-Value Work:
0.181 (Depositor)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7PK0

Ligand Structure Quality Assessment

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

Literature

Structure of glycine N-acyltransferase clarifies its catalytic mechanism

Ebrecht, A.C., Badenhorst, C.P.S., Read, R.J., Opperman, D.J., van Dijk, A.A.

To be published.

Macromolecule Content

Total Structure Weight: 34.93 kDa
Atom Count: 2,542
Modeled Residue Count: 284
Deposited Residue Count: 296
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine N-acyltransferase	A	296	Bos taurus	Mutation(s): 1 Gene Names: GLYAT EC: 2.3.1.13 (PDB Primary Data), 2.3.1.71 (PDB Primary Data)
UniProt
Find proteins for Q2KIR7 (Bos taurus) Explore Q2KIR7 Go to UniProtKB: Q2KIR7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2KIR7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BYC (Subject of Investigation/LOI) Query on BYC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	benzoyl coenzyme A C₂₈ H₄₀ N₇ O₁₇ P₃ S VEVJTUNLALKRNO-TYHXJLICSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.211 (Depositor), 0.217 (DCC)
R-Value Work: 0.181 (Depositor)
R-Value Observed: 0.182 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.84	α = 90
b = 63.84	β = 90
c = 135.336	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-09-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Global Challenges Research Fund	United Kingdom	ST/R002754/1

Revision History (Full details and data files)

Version 1.0: 2022-09-07
Type: Initial release
Version 1.1: 2024-06-19
Changes: Data collection

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.