8AJT | pdb_00008ajt

Crystal structure of the H323A mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa cocrystallized with adenosine in the presence of K+ cations

PDB DOI: https://doi.org/10.2210/pdb8AJT/pdb

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

Deposited: 2022-07-28 Released: 2023-08-16
Deposition Author(s): Drozdzal, P., Wozniak, K., Malecki, P., Gawel, M., Komorowska, M., Brzezinski, K.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.167 (Depositor), 0.167 (DCC)
R-Value Work:
0.152 (Depositor), 0.152 (DCC)

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 the H323A mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa cocrystallized with adenosine in the presence of K+ cations

Drozdzal, P., Wozniak, K., Malecki, P., Gawel, M., Komorowska, M., Brzezinski, K.

To be published.

Macromolecule Content

Total Structure Weight: 212.73 kDa
Atom Count: 16,457
Modeled Residue Count: 1,844
Deposited Residue Count: 1,888
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	472	Pseudomonas aeruginosa PAO1	Mutation(s): 1 Gene Names: ahcY, sahH, PA0432 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 7 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 F [auth AAA] SDF format, chain N [auth BBB] SDF format, chain U [auth CCC] SDF format, chain FA [auth DDD] MOL2 format, chain F [auth AAA] MOL2 format, chain N [auth BBB] MOL2 format, chain U [auth CCC] MOL2 format, chain FA [auth DDD] mmCIF format, chain F [auth AAA] mmCIF format, chain N [auth BBB] mmCIF format, chain U [auth CCC] mmCIF format, chain FA [auth DDD]	F [auth AAA], FA [auth DDD], N [auth BBB], U [auth CCC]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain F [auth AAA] Focus chain FA [auth DDD] Focus chain N [auth BBB] Focus chain U [auth CCC] Interactions & Density Focus chain F [auth AAA] Focus chain FA [auth DDD] Focus chain N [auth BBB] Focus chain U [auth CCC]
ADN (Subject of Investigation/LOI) Query on ADN Download:Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain EA [auth DDD] SDF format, chain M [auth BBB] SDF format, chain V [auth CCC] MOL2 format, chain E [auth AAA] MOL2 format, chain EA [auth DDD] MOL2 format, chain M [auth BBB] MOL2 format, chain V [auth CCC] mmCIF format, chain E [auth AAA] mmCIF format, chain EA [auth DDD] mmCIF format, chain M [auth BBB] mmCIF format, chain V [auth CCC]	E [auth AAA], EA [auth DDD], M [auth BBB], V [auth CCC]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain E [auth AAA] Focus chain EA [auth DDD] Focus chain M [auth BBB] Focus chain V [auth CCC] Interactions & Density Focus chain E [auth AAA] Focus chain EA [auth DDD] Focus chain M [auth BBB] Focus chain V [auth CCC]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain G [auth AAA] SDF format, chain IA [auth DDD] SDF format, chain P [auth BBB] SDF format, chain X [auth CCC] SDF format, chain W [auth CCC] SDF format, chain O [auth BBB] SDF format, chain H [auth AAA] SDF format, chain GA [auth DDD] MOL2 format, chain G [auth AAA] MOL2 format, chain IA [auth DDD] MOL2 format, chain P [auth BBB] MOL2 format, chain X [auth CCC] MOL2 format, chain W [auth CCC] MOL2 format, chain O [auth BBB] MOL2 format, chain H [auth AAA] MOL2 format, chain GA [auth DDD] mmCIF format, chain G [auth AAA] mmCIF format, chain IA [auth DDD] mmCIF format, chain P [auth BBB] mmCIF format, chain X [auth CCC] mmCIF format, chain W [auth CCC] mmCIF format, chain O [auth BBB] mmCIF format, chain H [auth AAA] mmCIF format, chain GA [auth DDD]	G [auth AAA] GA [auth DDD] H [auth AAA] IA [auth DDD] O [auth BBB] G [auth AAA], GA [auth DDD], H [auth AAA], IA [auth DDD], O [auth BBB], P [auth BBB], W [auth CCC], X [auth CCC]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain G [auth AAA] Focus chain GA [auth DDD] Focus chain H [auth AAA] Focus chain IA [auth DDD] Focus chain O [auth BBB] Focus chain P [auth BBB] Focus chain W [auth CCC] Focus chain X [auth CCC] Interactions & Density Focus chain G [auth AAA] Focus chain GA [auth DDD] Focus chain H [auth AAA] Focus chain IA [auth DDD] Focus chain O [auth BBB] Focus chain P [auth BBB] Focus chain W [auth CCC] Focus chain X [auth CCC]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain AA [auth CCC] SDF format, chain HA [auth DDD] SDF format, chain I [auth AAA] SDF format, chain Z [auth CCC] MOL2 format, chain AA [auth CCC] MOL2 format, chain HA [auth DDD] MOL2 format, chain I [auth AAA] MOL2 format, chain Z [auth CCC] mmCIF format, chain AA [auth CCC] mmCIF format, chain HA [auth DDD] mmCIF format, chain I [auth AAA] mmCIF format, chain Z [auth CCC]	AA [auth CCC], HA [auth DDD], I [auth AAA], Z [auth CCC]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth CCC] Focus chain HA [auth DDD] Focus chain I [auth AAA] Focus chain Z [auth CCC] Interactions & Density Focus chain AA [auth CCC] Focus chain HA [auth DDD] Focus chain I [auth AAA] Focus chain Z [auth CCC]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain CA [auth CCC] SDF format, chain K [auth AAA] SDF format, chain Y [auth CCC] SDF format, chain LA [auth DDD] MOL2 format, chain CA [auth CCC] MOL2 format, chain K [auth AAA] MOL2 format, chain Y [auth CCC] MOL2 format, chain LA [auth DDD] mmCIF format, chain CA [auth CCC] mmCIF format, chain K [auth AAA] mmCIF format, chain Y [auth CCC] mmCIF format, chain LA [auth DDD]	CA [auth CCC], K [auth AAA], LA [auth DDD], Y [auth CCC]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth CCC] Focus chain K [auth AAA] Focus chain LA [auth DDD] Focus chain Y [auth CCC] Interactions & Density Focus chain CA [auth CCC] Focus chain K [auth AAA] Focus chain LA [auth DDD] Focus chain Y [auth CCC]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain J [auth AAA] SDF format, chain KA [auth DDD] SDF format, chain Q [auth BBB] SDF format, chain JA [auth DDD] SDF format, chain BA [auth CCC] MOL2 format, chain J [auth AAA] MOL2 format, chain KA [auth DDD] MOL2 format, chain Q [auth BBB] MOL2 format, chain JA [auth DDD] MOL2 format, chain BA [auth CCC] mmCIF format, chain J [auth AAA] mmCIF format, chain KA [auth DDD] mmCIF format, chain Q [auth BBB] mmCIF format, chain JA [auth DDD] mmCIF format, chain BA [auth CCC]	BA [auth CCC], J [auth AAA], JA [auth DDD], KA [auth DDD], Q [auth BBB]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain BA [auth CCC] Focus chain J [auth AAA] Focus chain JA [auth DDD] Focus chain KA [auth DDD] Focus chain Q [auth BBB] Interactions & Density Focus chain BA [auth CCC] Focus chain J [auth AAA] Focus chain JA [auth DDD] Focus chain KA [auth DDD] Focus chain Q [auth BBB]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain DA [auth CCC] SDF format, chain QA [auth DDD] SDF format, chain S [auth BBB] SDF format, chain T [auth BBB] SDF format, chain R [auth BBB] SDF format, chain PA [auth DDD] SDF format, chain OA [auth DDD] SDF format, chain NA [auth DDD] SDF format, chain MA [auth DDD] SDF format, chain L [auth AAA] MOL2 format, chain DA [auth CCC] MOL2 format, chain QA [auth DDD] MOL2 format, chain S [auth BBB] MOL2 format, chain T [auth BBB] MOL2 format, chain R [auth BBB] MOL2 format, chain PA [auth DDD] MOL2 format, chain OA [auth DDD] MOL2 format, chain NA [auth DDD] MOL2 format, chain MA [auth DDD] MOL2 format, chain L [auth AAA] mmCIF format, chain DA [auth CCC] mmCIF format, chain QA [auth DDD] mmCIF format, chain S [auth BBB] mmCIF format, chain T [auth BBB] mmCIF format, chain R [auth BBB] mmCIF format, chain PA [auth DDD] mmCIF format, chain OA [auth DDD] mmCIF format, chain NA [auth DDD] mmCIF format, chain MA [auth DDD] mmCIF format, chain L [auth AAA]	DA [auth CCC] L [auth AAA] MA [auth DDD] NA [auth DDD] OA [auth DDD] DA [auth CCC], L [auth AAA], MA [auth DDD], NA [auth DDD], OA [auth DDD], PA [auth DDD], QA [auth DDD], R [auth BBB], S [auth BBB], T [auth BBB]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth CCC] Focus chain L [auth AAA] Focus chain MA [auth DDD] Focus chain NA [auth DDD] Focus chain OA [auth DDD] Focus chain PA [auth DDD] Focus chain QA [auth DDD] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB] Interactions & Density Focus chain DA [auth CCC] Focus chain L [auth AAA] Focus chain MA [auth DDD] Focus chain NA [auth DDD] Focus chain OA [auth DDD] Focus chain PA [auth DDD] Focus chain QA [auth DDD] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB]