8CFV

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment H04

PDB DOI: https://doi.org/10.2210/pdb8CFV/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: 1.88 Å
R-Value Free: 0.202
R-Value Work: 0.160
R-Value Observed: 0.160

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 H04

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

To be published.

Macromolecule Content

Total Structure Weight: 212.45 kDa
Atom Count: 16,209
Modelled Residue Count: 1,847
Deposited Residue Count: 1,888
Unique protein chains: 1

Macromolecules

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(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 (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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain O [auth B] SDF format, chain X [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain X [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain X [auth C]	E [auth A], EA [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 EA [auth D] Focus chain O [auth B] Focus chain X [auth C] Interactions & Density Focus chain E [auth A] Focus chain EA [auth D] Focus chain O [auth B] Focus chain X [auth C]
3S9 (Subject of Investigation/LOI) Query on 3S9 Download Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	benzyl (cyanomethyl)carbamate C₁₀ H₁₀ N₂ O₂ DVUXKEFDAGQPQU-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
ADE Query on ADE Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain P [auth B] SDF format, chain Y [auth C] SDF format, chain FA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain FA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain FA [auth D]	F [auth A], FA [auth D], P [auth B], Y [auth C]	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain FA [auth D] Focus chain P [auth B] Focus chain Y [auth C] Interactions & Density Focus chain F [auth A] Focus chain FA [auth D] Focus chain P [auth B] Focus chain Y [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain I [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain AA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain U [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain U [auth B]	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], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], U [auth B], V [auth B], W [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 IA [auth D] 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 U [auth B] Focus chain V [auth B] Focus chain W [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 IA [auth D] 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 U [auth B] Focus chain V [auth B] Focus chain W [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain N [auth B] MOL2 format, chain GA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain N [auth B] mmCIF format, chain GA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain N [auth B]	GA [auth D], N [auth B], Q [auth B], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GA [auth D] Focus chain N [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain GA [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 G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain T [auth B] SDF format, chain Z [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain Z [auth C]	H [auth A], HA [auth D], T [auth B], Z [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain HA [auth D] Focus chain T [auth B] Focus chain Z [auth C] Interactions & Density Focus chain H [auth A] Focus chain HA [auth D] Focus chain T [auth B] Focus chain Z [auth C]