7PK2 | pdb_00007pk2

Bovine Glycine N-Acyltransferase

PDB DOI: https://doi.org/10.2210/pdb7PK2/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: 1.25 Å
R-Value Free:
0.200 (Depositor), 0.210 (DCC)
R-Value Work:
0.177 (Depositor), 0.190 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

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: 68.2 kDa
Atom Count: 5,296
Modeled Residue Count: 568
Deposited Residue Count: 592
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine N-acyltransferase	A, B	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.200 (Depositor), 0.210 (DCC)
R-Value Work: 0.177 (Depositor), 0.190 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.112	α = 90
b = 63.587	β = 90
c = 135.503	γ = 90

Software Package:

Software Name	Purpose
xia2	data reduction
XSCALE	data scaling
SHELXD	phasing
CRANK2	phasing
HKL2Map	model building
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.