8IZJ | pdb_00008izj

Crystal structure of Escherichia coli Adenine Phosphoribosyltransferase (APRT) in complex with AMP

PDB DOI: https://doi.org/10.2210/pdb8IZJ/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-04-07 Released: 2024-04-10
Deposition Author(s): Yadav, P., Kushwaha, G.S., Bhavesh, N.S.
Funding Organization(s): Indian Council of Medical Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.192 (Depositor), 0.204 (DCC)
R-Value Work:
0.165 (Depositor), 0.177 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Escherichia coli Adenine Phosphoribosyltransferase (APRT) in complex with AMP

Yadav, P., Kushwaha, G.S., Bhavesh, N.S.

To be published.

Macromolecule Content

Total Structure Weight: 41.3 kDa
Atom Count: 3,341
Modeled Residue Count: 365
Deposited Residue Count: 372
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine phosphoribosyltransferase	A, B	186	Escherichia coli	Mutation(s): 0 Gene Names: apt, b0469, JW0458 EC: 2.4.2.7
UniProt
Find proteins for P69503 (Escherichia coli (strain K12)) Explore P69503 Go to UniProtKB: P69503
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69503
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]