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
Modelled 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 LOADING

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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	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.