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), 0.220 (DCC)
R-Value Work:
0.181 (Depositor), 0.190 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

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

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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), 0.220 (DCC)
R-Value Work: 0.181 (Depositor), 0.190 (DCC)
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

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Ligand Structure Quality Assessment

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 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.