8AZF | pdb_00008azf

Crystal structure of K449E variant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa in complex with adenosine

PDB DOI: https://doi.org/10.2210/pdb8AZF/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-09-06 Released: 2023-09-13
Deposition Author(s): Arning, A., Malecki, P., Wozniak, K., Brzezinski, K.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free:
0.225 (Depositor), 0.224 (DCC)
R-Value Work:
0.167 (Depositor), 0.167 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of K449E variant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa in complex with adenosine

Arning, A., Malecki, P., Wozniak, K., Brzezinski, K.

To be published.

Macromolecule Content

Total Structure Weight: 105.6 kDa
Atom Count: 9,227
Modeled Residue Count: 920
Deposited Residue Count: 944
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B [auth C]	472	Pseudomonas aeruginosa PAO1	Mutation(s): 1 Gene Names: ahcY, PLES_04301 EC: 3.3.1.1 (PDB Primary Data), 3.13.2.1 (UniProt)
UniProt
Find proteins for Q9I685 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I685 Go to UniProtKB: Q9I685
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I685
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth C] MOL2 format, chain C [auth A] MOL2 format, chain G [auth C] mmCIF format, chain C [auth A] mmCIF format, chain G [auth C]	C [auth A], G [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain G [auth C] Interactions & Density Focus chain C [auth A] Focus chain G [auth C]
ADN (Subject of Investigation/LOI) Query on ADN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth C] mmCIF format, chain D [auth A] mmCIF format, chain H [auth C]	D [auth A], H [auth C]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C]	F [auth A], J [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain J [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth C]
K (Subject of Investigation/LOI) Query on K Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain E [auth A] MOL2 format, chain I [auth C] MOL2 format, chain E [auth A] mmCIF format, chain I [auth C] mmCIF format, chain E [auth A]	E [auth A], I [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth C]