8AJV

Crystal structure of the Q65N mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa crystallized in the presence of K+ cations

PDB DOI: https://doi.org/10.2210/pdb8AJV/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: 1.90 Å
R-Value Free:
0.194 (Depositor), 0.200 (DCC)
R-Value Work:
0.160 (Depositor), 0.170 (DCC)

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 the Q65N mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa crystallized 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: 422.71 kDa
Atom Count: 32,384
Modelled Residue Count: 3,688
Deposited Residue Count: 3,776
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 [auth AAA] B [auth BBB] C [auth CCC] D [auth DDD] E [auth FFF] A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth FFF], F [auth GGG], G [auth HHH], H [auth III]	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I685
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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 AB [auth III] SDF format, chain CA [auth DDD] SDF format, chain I [auth AAA] SDF format, chain MA [auth FFF] SDF format, chain N [auth BBB] SDF format, chain RA [auth GGG] SDF format, chain VA [auth HHH] SDF format, chain W [auth CCC] MOL2 format, chain AB [auth III] MOL2 format, chain CA [auth DDD] MOL2 format, chain I [auth AAA] MOL2 format, chain MA [auth FFF] MOL2 format, chain N [auth BBB] MOL2 format, chain RA [auth GGG] MOL2 format, chain VA [auth HHH] MOL2 format, chain W [auth CCC] mmCIF format, chain AB [auth III] mmCIF format, chain CA [auth DDD] mmCIF format, chain I [auth AAA] mmCIF format, chain MA [auth FFF] mmCIF format, chain N [auth BBB] mmCIF format, chain RA [auth GGG] mmCIF format, chain VA [auth HHH] mmCIF format, chain W [auth CCC]	AB [auth III] CA [auth DDD] I [auth AAA] MA [auth FFF] N [auth BBB] AB [auth III], CA [auth DDD], I [auth AAA], MA [auth FFF], N [auth BBB], RA [auth GGG], VA [auth HHH], W [auth CCC]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AB [auth III] Focus chain CA [auth DDD] Focus chain I [auth AAA] Focus chain MA [auth FFF] Focus chain N [auth BBB] Focus chain RA [auth GGG] Focus chain VA [auth HHH] Focus chain W [auth CCC] Interactions & Density Focus chain AB [auth III] Focus chain CA [auth DDD] Focus chain I [auth AAA] Focus chain MA [auth FFF] Focus chain N [auth BBB] Focus chain RA [auth GGG] Focus chain VA [auth HHH] Focus chain W [auth CCC]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth CCC] SDF format, chain BA [auth CCC] MOL2 format, chain AA [auth CCC] MOL2 format, chain BA [auth CCC] mmCIF format, chain AA [auth CCC] mmCIF format, chain BA [auth CCC]	AA [auth CCC], BA [auth CCC]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth CCC] Focus chain BA [auth CCC] Interactions & Density Focus chain AA [auth CCC] Focus chain BA [auth CCC]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain GA [auth DDD] SDF format, chain HA [auth DDD] SDF format, chain IA [auth DDD] SDF format, chain K [auth AAA] SDF format, chain KA [auth FFF] SDF format, chain L [auth AAA] SDF format, chain LA [auth FFF] SDF format, chain M [auth AAA] SDF format, chain NA [auth GGG] SDF format, chain OA [auth GGG] SDF format, chain PA [auth GGG] SDF format, chain QA [auth GGG] SDF format, chain R [auth BBB] SDF format, chain S [auth BBB] SDF format, chain T [auth BBB] SDF format, chain TA [auth HHH] SDF format, chain U [auth BBB] SDF format, chain UA [auth HHH] SDF format, chain XA [auth III] SDF format, chain Y [auth CCC] SDF format, chain YA [auth III] SDF format, chain Z [auth CCC] SDF format, chain ZA [auth III] SDF format, chain JA [auth FFF] MOL2 format, chain GA [auth DDD] MOL2 format, chain HA [auth DDD] MOL2 format, chain IA [auth DDD] MOL2 format, chain K [auth AAA] MOL2 format, chain KA [auth FFF] MOL2 format, chain L [auth AAA] MOL2 format, chain LA [auth FFF] MOL2 format, chain M [auth AAA] MOL2 format, chain NA [auth GGG] MOL2 format, chain OA [auth GGG] MOL2 format, chain PA [auth GGG] MOL2 format, chain QA [auth GGG] MOL2 format, chain R [auth BBB] MOL2 format, chain S [auth BBB] MOL2 format, chain T [auth BBB] MOL2 format, chain TA [auth HHH] MOL2 format, chain U [auth BBB] MOL2 format, chain UA [auth HHH] MOL2 format, chain XA [auth III] MOL2 format, chain Y [auth CCC] MOL2 format, chain YA [auth III] MOL2 format, chain Z [auth CCC] MOL2 format, chain ZA [auth III] MOL2 format, chain JA [auth FFF] mmCIF format, chain GA [auth DDD] mmCIF format, chain HA [auth DDD] mmCIF format, chain IA [auth DDD] mmCIF format, chain K [auth AAA] mmCIF format, chain KA [auth FFF] mmCIF format, chain L [auth AAA] mmCIF format, chain LA [auth FFF] mmCIF format, chain M [auth AAA] mmCIF format, chain NA [auth GGG] mmCIF format, chain OA [auth GGG] mmCIF format, chain PA [auth GGG] mmCIF format, chain QA [auth GGG] mmCIF format, chain R [auth BBB] mmCIF format, chain S [auth BBB] mmCIF format, chain T [auth BBB] mmCIF format, chain TA [auth HHH] mmCIF format, chain U [auth BBB] mmCIF format, chain UA [auth HHH] mmCIF format, chain XA [auth III] mmCIF format, chain Y [auth CCC] mmCIF format, chain YA [auth III] mmCIF format, chain Z [auth CCC] mmCIF format, chain ZA [auth III] mmCIF format, chain JA [auth FFF]	GA [auth DDD] HA [auth DDD] IA [auth DDD] JA [auth FFF] K [auth AAA] GA [auth DDD], HA [auth DDD], IA [auth DDD], JA [auth FFF], K [auth AAA], KA [auth FFF], L [auth AAA], LA [auth FFF], M [auth AAA], NA [auth GGG], OA [auth GGG], PA [auth GGG], QA [auth GGG], R [auth BBB], S [auth BBB], T [auth BBB], TA [auth HHH], U [auth BBB], UA [auth HHH], XA [auth III], Y [auth CCC], YA [auth III], Z [auth CCC], ZA [auth III]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain GA [auth DDD] Focus chain HA [auth DDD] Focus chain IA [auth DDD] Focus chain JA [auth FFF] Focus chain K [auth AAA] Focus chain KA [auth FFF] Focus chain L [auth AAA] Focus chain LA [auth FFF] Focus chain M [auth AAA] Focus chain NA [auth GGG] Focus chain OA [auth GGG] Focus chain PA [auth GGG] Focus chain QA [auth GGG] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB] Focus chain TA [auth HHH] Focus chain U [auth BBB] Focus chain UA [auth HHH] Focus chain XA [auth III] Focus chain Y [auth CCC] Focus chain YA [auth III] Focus chain Z [auth CCC] Focus chain ZA [auth III] Interactions & Density Focus chain GA [auth DDD] Focus chain HA [auth DDD] Focus chain IA [auth DDD] Focus chain JA [auth FFF] Focus chain K [auth AAA] Focus chain KA [auth FFF] Focus chain L [auth AAA] Focus chain LA [auth FFF] Focus chain M [auth AAA] Focus chain NA [auth GGG] Focus chain OA [auth GGG] Focus chain PA [auth GGG] Focus chain QA [auth GGG] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB] Focus chain TA [auth HHH] Focus chain U [auth BBB] Focus chain UA [auth HHH] Focus chain XA [auth III] Focus chain Y [auth CCC] Focus chain YA [auth III] Focus chain Z [auth CCC] Focus chain ZA [auth III]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BB [auth III] SDF format, chain CB [auth III] SDF format, chain DA [auth DDD] SDF format, chain EA [auth DDD] SDF format, chain FA [auth DDD] SDF format, chain J [auth AAA] SDF format, chain P [auth BBB] SDF format, chain Q [auth BBB] SDF format, chain SA [auth GGG] SDF format, chain WA [auth HHH] SDF format, chain X [auth CCC] SDF format, chain O [auth BBB] MOL2 format, chain BB [auth III] MOL2 format, chain CB [auth III] MOL2 format, chain DA [auth DDD] MOL2 format, chain EA [auth DDD] MOL2 format, chain FA [auth DDD] MOL2 format, chain J [auth AAA] MOL2 format, chain P [auth BBB] MOL2 format, chain Q [auth BBB] MOL2 format, chain SA [auth GGG] MOL2 format, chain WA [auth HHH] MOL2 format, chain X [auth CCC] MOL2 format, chain O [auth BBB] mmCIF format, chain BB [auth III] mmCIF format, chain CB [auth III] mmCIF format, chain DA [auth DDD] mmCIF format, chain EA [auth DDD] mmCIF format, chain FA [auth DDD] mmCIF format, chain J [auth AAA] mmCIF format, chain P [auth BBB] mmCIF format, chain Q [auth BBB] mmCIF format, chain SA [auth GGG] mmCIF format, chain WA [auth HHH] mmCIF format, chain X [auth CCC] mmCIF format, chain O [auth BBB]	BB [auth III] CB [auth III] DA [auth DDD] EA [auth DDD] FA [auth DDD] BB [auth III], CB [auth III], DA [auth DDD], EA [auth DDD], FA [auth DDD], J [auth AAA], O [auth BBB], P [auth BBB], Q [auth BBB], SA [auth GGG], WA [auth HHH], X [auth CCC]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BB [auth III] Focus chain CB [auth III] Focus chain DA [auth DDD] Focus chain EA [auth DDD] Focus chain FA [auth DDD] Focus chain J [auth AAA] Focus chain O [auth BBB] Focus chain P [auth BBB] Focus chain Q [auth BBB] Focus chain SA [auth GGG] Focus chain WA [auth HHH] Focus chain X [auth CCC] Interactions & Density Focus chain BB [auth III] Focus chain CB [auth III] Focus chain DA [auth DDD] Focus chain EA [auth DDD] Focus chain FA [auth DDD] Focus chain J [auth AAA] Focus chain O [auth BBB] Focus chain P [auth BBB] Focus chain Q [auth BBB] Focus chain SA [auth GGG] Focus chain WA [auth HHH] Focus chain X [auth CCC]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain V [auth BBB] MOL2 format, chain V [auth BBB] mmCIF format, chain V [auth BBB]	V [auth BBB]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain V [auth BBB] Interactions & Density Focus chain V [auth BBB]