8CFM | pdb_00008cfm

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment E08

PDB DOI: https://doi.org/10.2210/pdb8CFM/pdb

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

Deposited: 2023-02-03 Released: 2024-02-21
Deposition Author(s): Malecki, P.H., Gawel, M., Stepniewska, M., Brzezinski, K.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.201 (Depositor), 0.201 (DCC)
R-Value Work:
0.167 (Depositor), 0.167 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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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 S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with fragment F2X-Entry E08

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

To be published.

Macromolecule Content

Total Structure Weight: 212.54 kDa
Atom Count: 16,246
Modeled Residue Count: 1,847
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, B, C, D	472	Pseudomonas aeruginosa PAO1	Mutation(s): 0 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 Query on NAD Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain O [auth B] SDF format, chain FA [auth D] SDF format, chain E [auth A] MOL2 format, chain X [auth C] MOL2 format, chain O [auth B] MOL2 format, chain FA [auth D] MOL2 format, chain E [auth A] mmCIF format, chain X [auth C] mmCIF format, chain O [auth B] mmCIF format, chain FA [auth D] mmCIF format, chain E [auth A]	E [auth A], FA [auth D], O [auth B], X [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain FA [auth D] Focus chain O [auth B] Focus chain X [auth C] Interactions & Density Focus chain E [auth A] Focus chain FA [auth D] Focus chain O [auth B] Focus chain X [auth C]
UHL (Subject of Investigation/LOI) Query on UHL Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain G [auth A] MOL2 format, chain W [auth C] MOL2 format, chain G [auth A] mmCIF format, chain W [auth C] mmCIF format, chain G [auth A]	G [auth A], W [auth C]	5-(2-methoxyethyl)-1,3,4-oxadiazol-2-amine C₅ H₉ N₃ O₂ NOHAGGWBLILEEG-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain W [auth C] Interactions & Density Focus chain G [auth A] Focus chain W [auth C]
ADE Query on ADE Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain P [auth B] SDF format, chain GA [auth D] SDF format, chain F [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain P [auth B] MOL2 format, chain GA [auth D] MOL2 format, chain F [auth A] mmCIF format, chain Y [auth C] mmCIF format, chain P [auth B] mmCIF format, chain GA [auth D] mmCIF format, chain F [auth A]	F [auth A], GA [auth D], P [auth B], Y [auth C]	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain GA [auth D] Focus chain P [auth B] Focus chain Y [auth C] Interactions & Density Focus chain F [auth A] Focus chain GA [auth D] Focus chain P [auth B] Focus chain Y [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain MA [auth D] SDF format, chain M [auth A] SDF format, chain LA [auth D] SDF format, chain L [auth A] SDF format, chain KA [auth D] SDF format, chain K [auth A] SDF format, chain JA [auth D] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain MA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain MA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] I [auth A] AA [auth C], BA [auth C], CA [auth C], DA [auth C], I [auth A], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], T [auth B], U [auth B], V [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain N [auth B] SDF format, chain HA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth B] MOL2 format, chain HA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth B] mmCIF format, chain HA [auth D]	HA [auth D], N [auth B], Q [auth B], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain HA [auth D] Focus chain N [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain HA [auth D] Focus chain N [auth B] Focus chain Q [auth B] Focus chain R [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] MOL2 format, chain EA [auth D] mmCIF format, chain EA [auth D]	EA [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Interactions & Density Focus chain EA [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain Z [auth C] SDF format, chain S [auth B] SDF format, chain H [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain S [auth B] MOL2 format, chain H [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain S [auth B] mmCIF format, chain H [auth A]	H [auth A], IA [auth D], S [auth B], Z [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain IA [auth D] Focus chain S [auth B] Focus chain Z [auth C] Interactions & Density Focus chain H [auth A] Focus chain IA [auth D] Focus chain S [auth B] Focus chain Z [auth C]