7CIV | pdb_00007civ

Crystal Structure of Agmatine N-Acetyltransferase mutant S171A in complex with Ac-CoA

PDB DOI: https://doi.org/10.2210/pdb7CIV/pdb

Classification: TRANSFERASE
Organism(s): Drosophila melanogaster
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-07-08 Released: 2021-08-18
Deposition Author(s): Chen, J.J., Hu, I.C., Lai, C.H., Lyu, P.C.
Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.241 (Depositor), 0.241 (DCC)
R-Value Work:
0.191 (Depositor), 0.191 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Agmatine N-Acetyltransferase mutant S171A in complex with Ac-CoA

Chen, J.J., Hu, I.C., Lai, C.H., Lyu, P.C.

To be published.

Macromolecule Content

Total Structure Weight: 24.59 kDa
Atom Count: 1,826
Modeled Residue Count: 215
Deposited Residue Count: 216
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agmatine N-acetyltransferase	A	216	Drosophila melanogaster	Mutation(s): 1 Gene Names: AgmNAT, AANATL8, Dmel\CG15766, CG15766, Dmel_CG15766 EC: 2.3.1.5 (PDB Primary Data), 2.3.1.87 (UniProt)
UniProt
Find proteins for Q9W469 (Drosophila melanogaster) Explore Q9W469 Go to UniProtKB: Q9W469
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9W469
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO (Subject of Investigation/LOI) Query on ACO 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]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.241 (Depositor), 0.241 (DCC)
R-Value Work: 0.191 (Depositor), 0.191 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.202	α = 90
b = 51.676	β = 90
c = 81.928	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-08-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History (Full details and data files)

Version 1.0: 2021-08-18
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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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.