8AJV | pdb_00008ajv

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), 0.202 (DCC)
R-Value Work:
0.160 (Depositor), 0.167 (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 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
Modeled Residue Count: 3,688
Deposited Residue Count: 3,776
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] 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 I [auth AAA] SDF format, chain N [auth BBB] SDF format, chain VA [auth HHH] SDF format, chain W [auth CCC] SDF format, chain RA [auth GGG] SDF format, chain MA [auth FFF] SDF format, chain CA [auth DDD] MOL2 format, chain AB [auth III] MOL2 format, chain I [auth AAA] MOL2 format, chain N [auth BBB] MOL2 format, chain VA [auth HHH] MOL2 format, chain W [auth CCC] MOL2 format, chain RA [auth GGG] MOL2 format, chain MA [auth FFF] MOL2 format, chain CA [auth DDD] mmCIF format, chain AB [auth III] mmCIF format, chain I [auth AAA] mmCIF format, chain N [auth BBB] mmCIF format, chain VA [auth HHH] mmCIF format, chain W [auth CCC] mmCIF format, chain RA [auth GGG] mmCIF format, chain MA [auth FFF] mmCIF format, chain CA [auth DDD]	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 BA [auth CCC] SDF format, chain AA [auth CCC] MOL2 format, chain BA [auth CCC] MOL2 format, chain AA [auth CCC] mmCIF format, chain BA [auth CCC] mmCIF format, chain AA [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 JA [auth FFF] 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 K [auth AAA] MOL2 format, chain GA [auth DDD] MOL2 format, chain HA [auth DDD] MOL2 format, chain IA [auth DDD] MOL2 format, chain JA [auth FFF] 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 K [auth AAA] mmCIF format, chain GA [auth DDD] mmCIF format, chain HA [auth DDD] mmCIF format, chain IA [auth DDD] mmCIF format, chain JA [auth FFF] 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 K [auth AAA]	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 O [auth BBB] SDF format, chain P [auth BBB] SDF format, chain Q [auth BBB] SDF format, chain SA [auth GGG] SDF format, chain X [auth CCC] SDF format, chain WA [auth HHH] SDF format, chain J [auth AAA] 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 O [auth BBB] MOL2 format, chain P [auth BBB] MOL2 format, chain Q [auth BBB] MOL2 format, chain SA [auth GGG] MOL2 format, chain X [auth CCC] MOL2 format, chain WA [auth HHH] MOL2 format, chain J [auth AAA] 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 O [auth BBB] mmCIF format, chain P [auth BBB] mmCIF format, chain Q [auth BBB] mmCIF format, chain SA [auth GGG] mmCIF format, chain X [auth CCC] mmCIF format, chain WA [auth HHH] mmCIF format, chain J [auth AAA]	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]