7ZD3

Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocysteine hydrolase inhibited by Zn2+ ions

PDB DOI: https://doi.org/10.2210/pdb7ZD3/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-29 Released: 2023-04-19
Deposition Author(s): Malecki, P.H., Gawel, M., Brzezinski, K.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.222
R-Value Work: 0.180
R-Value Observed: 0.180

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 Pseudomonas aeruginosa S-adenosyl-L-homocysteine hydrolase inhibited by Zn2+ ions

Malecki, P.H., Gawel, M., Brzezinski, K.

To be published.

Macromolecule Content

Total Structure Weight: 213.17 kDa
Atom Count: 16,660
Modelled Residue Count: 1,842
Deposited Residue Count: 1,888
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B, C, D	472	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: ahcY, sahH, PA0432 EC: 3.3.1.1
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I685
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 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 AA [auth C] SDF format, chain E [auth A] SDF format, chain KA [auth D] SDF format, chain P [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain P [auth B]	AA [auth C], E [auth A], KA [auth D], P [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth C] Focus chain E [auth A] Focus chain KA [auth D] Focus chain P [auth B] Interactions & Density Focus chain AA [auth C] Focus chain E [auth A] Focus chain KA [auth D] Focus chain P [auth B]
ADN (Subject of Investigation/LOI) Query on ADN Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain F [auth A] SDF format, chain LA [auth D] SDF format, chain Q [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain Q [auth B]	BA [auth C], F [auth A], LA [auth D], Q [auth B]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain BA [auth C] Focus chain F [auth A] Focus chain LA [auth D] Focus chain Q [auth B] Interactions & Density Focus chain BA [auth C] Focus chain F [auth A] Focus chain LA [auth D] Focus chain Q [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
BCN Query on BCN Download Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B]	Y [auth B]	BICINE C₆ H₁₃ N O₄ FSVCELGFZIQNCK-UHFFFAOYSA-N		Interactions Focus chain Y [auth B] Interactions & Density Focus chain Y [auth B]
HEZ Query on HEZ Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain Z [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain Z [auth C]	EA [auth C], Z [auth C]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain Z [auth C] Interactions & Density Focus chain EA [auth C] Focus chain Z [auth C]
BU1 Query on BU1 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B]	G [auth A], H [auth A], J [auth A], R [auth B], S [auth B]	1,4-BUTANEDIOL C₄ H₁₀ O₂ WERYXYBDKMZEQL-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B]
PDO Query on PDO Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain FA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain FA [auth C]	CA [auth C], DA [auth C], FA [auth C]	1,3-PROPANDIOL C₃ H₈ O₂ YPFDHNVEDLHUCE-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FA [auth C] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FA [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	HA [auth C] IA [auth C] JA [auth C] L [auth A] M [auth A] HA [auth C], IA [auth C], JA [auth C], L [auth A], M [auth A], N [auth A], NA [auth D], O [auth A], OA [auth D], PA [auth D], QA [auth D], RA [auth D], U [auth B], V [auth B], W [auth B], X [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain K [auth A] SDF format, chain MA [auth D] SDF format, chain T [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain T [auth B]	GA [auth C], K [auth A], MA [auth D], T [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain K [auth A] Focus chain MA [auth D] Focus chain T [auth B] Interactions & Density Focus chain GA [auth C] Focus chain K [auth A] Focus chain MA [auth D] Focus chain T [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain SA [auth D] MOL2 format, chain SA [auth D]	SA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain SA [auth D] Interactions & Density Focus chain SA [auth D]