7CIW | pdb_00007ciw

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

PDB DOI: https://doi.org/10.2210/pdb7CIW/pdb

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

Deposited: 2020-07-08 Released: 2021-07-21
Deposition Author(s): Chen, J.J., Hu, I.C., Wu, C.Y., Lyu, P.C.
Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.234 (Depositor), 0.230 (DCC)
R-Value Work:
0.184 (Depositor), 0.180 (DCC)
R-Value Observed:
0.189 (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-Agm and CoA

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

To be published.

Macromolecule Content

Total Structure Weight: 24.72 kDa
Atom Count: 1,887
Modeled Residue Count: 216
Deposited Residue Count: 216
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9W469
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA 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]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
G0R (Subject of Investigation/LOI) Query on G0R 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]	N-(4-carbamimidamidobutyl)ethanamide C₇ H₁₆ N₄ O JMACEDIUUMWDIC-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.234 (Depositor), 0.230 (DCC)
R-Value Work: 0.184 (Depositor), 0.180 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.911	α = 90
b = 51.235	β = 90
c = 78.459	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

Entry History & Funding Information

Deposition Data

Released Date: 2021-07-21

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2021-07-21
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

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.