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
View more details

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

Find similar proteins by:

| 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 U [auth CCC] SDF format, chain N [auth BBB] SDF format, chain FA [auth DDD] SDF format, chain F [auth AAA] MOL2 format, chain U [auth CCC] MOL2 format, chain N [auth BBB] MOL2 format, chain FA [auth DDD] MOL2 format, chain F [auth AAA] mmCIF format, chain U [auth CCC] mmCIF format, chain N [auth BBB] mmCIF format, chain FA [auth DDD] mmCIF format, chain F [auth AAA]	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 V [auth CCC] SDF format, chain M [auth BBB] SDF format, chain EA [auth DDD] SDF format, chain E [auth AAA] MOL2 format, chain V [auth CCC] MOL2 format, chain M [auth BBB] MOL2 format, chain EA [auth DDD] MOL2 format, chain E [auth AAA] mmCIF format, chain V [auth CCC] mmCIF format, chain M [auth BBB] mmCIF format, chain EA [auth DDD] mmCIF format, chain E [auth AAA]	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 X [auth CCC] SDF format, chain W [auth CCC] SDF format, chain P [auth BBB] SDF format, chain O [auth BBB] SDF format, chain IA [auth DDD] SDF format, chain H [auth AAA] SDF format, chain GA [auth DDD] SDF format, chain G [auth AAA] MOL2 format, chain X [auth CCC] MOL2 format, chain W [auth CCC] MOL2 format, chain P [auth BBB] MOL2 format, chain O [auth BBB] MOL2 format, chain IA [auth DDD] MOL2 format, chain H [auth AAA] MOL2 format, chain GA [auth DDD] MOL2 format, chain G [auth AAA] mmCIF format, chain X [auth CCC] mmCIF format, chain W [auth CCC] mmCIF format, chain P [auth BBB] mmCIF format, chain O [auth BBB] mmCIF format, chain IA [auth DDD] mmCIF format, chain H [auth AAA] mmCIF format, chain GA [auth DDD] mmCIF format, chain G [auth AAA]	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 Z [auth CCC] SDF format, chain I [auth AAA] SDF format, chain HA [auth DDD] SDF format, chain AA [auth CCC] MOL2 format, chain Z [auth CCC] MOL2 format, chain I [auth AAA] MOL2 format, chain HA [auth DDD] MOL2 format, chain AA [auth CCC] mmCIF format, chain Z [auth CCC] mmCIF format, chain I [auth AAA] mmCIF format, chain HA [auth DDD] mmCIF format, chain AA [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 Y [auth CCC] SDF format, chain LA [auth DDD] SDF format, chain K [auth AAA] SDF format, chain CA [auth CCC] MOL2 format, chain Y [auth CCC] MOL2 format, chain LA [auth DDD] MOL2 format, chain K [auth AAA] MOL2 format, chain CA [auth CCC] mmCIF format, chain Y [auth CCC] mmCIF format, chain LA [auth DDD] mmCIF format, chain K [auth AAA] mmCIF format, chain CA [auth CCC]	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 Q [auth BBB] SDF format, chain KA [auth DDD] SDF format, chain JA [auth DDD] SDF format, chain J [auth AAA] SDF format, chain BA [auth CCC] MOL2 format, chain Q [auth BBB] MOL2 format, chain KA [auth DDD] MOL2 format, chain JA [auth DDD] MOL2 format, chain J [auth AAA] MOL2 format, chain BA [auth CCC] mmCIF format, chain Q [auth BBB] mmCIF format, chain KA [auth DDD] mmCIF format, chain JA [auth DDD] mmCIF format, chain J [auth AAA] 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 T [auth BBB] SDF format, chain S [auth BBB] SDF format, chain R [auth BBB] SDF format, chain QA [auth DDD] 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] SDF format, chain DA [auth CCC] MOL2 format, chain T [auth BBB] MOL2 format, chain S [auth BBB] MOL2 format, chain R [auth BBB] MOL2 format, chain QA [auth DDD] 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] MOL2 format, chain DA [auth CCC] mmCIF format, chain T [auth BBB] mmCIF format, chain S [auth BBB] mmCIF format, chain R [auth BBB] mmCIF format, chain QA [auth DDD] 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] mmCIF format, chain DA [auth CCC]	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]