8CFZ | pdb_00008cfz

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment H09

PDB DOI: https://doi.org/10.2210/pdb8CFZ/pdb

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

Deposited: 2023-02-03 Released: 2024-05-22
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: 1.77 Å
R-Value Free:
0.192 (Depositor), 0.192 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.170 (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 H09

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

To be published.

Macromolecule Content

Total Structure Weight: 424.7 kDa
Atom Count: 33,061
Modeled Residue Count: 3,691
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 B C D E [auth H] A, B, C, D, E [auth H], F [auth I], G [auth J], H [auth K]	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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain AB [auth J] SDF format, chain EA [auth D] SDF format, chain I [auth A] SDF format, chain MA [auth H] SDF format, chain MB [auth K] SDF format, chain P [auth B] SDF format, chain TA [auth I] SDF format, chain X [auth C] MOL2 format, chain AB [auth J] MOL2 format, chain EA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain MB [auth K] MOL2 format, chain P [auth B] MOL2 format, chain TA [auth I] MOL2 format, chain X [auth C] mmCIF format, chain AB [auth J] mmCIF format, chain EA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain MA [auth H] mmCIF format, chain MB [auth K] mmCIF format, chain P [auth B] mmCIF format, chain TA [auth I] mmCIF format, chain X [auth C]	AB [auth J] EA [auth D] I [auth A] MA [auth H] MB [auth K] AB [auth J], EA [auth D], I [auth A], MA [auth H], MB [auth K], P [auth B], TA [auth I], X [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AB [auth J] Focus chain EA [auth D] Focus chain I [auth A] Focus chain MA [auth H] Focus chain MB [auth K] Focus chain P [auth B] Focus chain TA [auth I] Focus chain X [auth C] Interactions & Density Focus chain AB [auth J] Focus chain EA [auth D] Focus chain I [auth A] Focus chain MA [auth H] Focus chain MB [auth K] Focus chain P [auth B] Focus chain TA [auth I] Focus chain X [auth C]
A1H8H (Subject of Investigation/LOI) Query on A1H8H Download:Ideal Coordinates CCD File SDF format, chain LA [auth D] SDF format, chain LB [auth K] SDF format, chain W [auth C] SDF format, chain ZA [auth I] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth K] MOL2 format, chain W [auth C] MOL2 format, chain ZA [auth I] mmCIF format, chain LA [auth D] mmCIF format, chain LB [auth K] mmCIF format, chain W [auth C] mmCIF format, chain ZA [auth I]	LA [auth D], LB [auth K], W [auth C], ZA [auth I]	1-[2,4-bis(fluoranyl)phenyl]-2-(3,4-dihydro-1,2,4-triazol-2-yl)ethanone C₁₀ H₉ F₂ N₃ O UWNAFSDCDMGFTR-UHFFFAOYSA-N		Interactions Focus chain LA [auth D] Focus chain LB [auth K] Focus chain W [auth C] Focus chain ZA [auth I] Interactions & Density Focus chain LA [auth D] Focus chain LB [auth K] Focus chain W [auth C] Focus chain ZA [auth I]
ADE Query on ADE Download:Ideal Coordinates CCD File SDF format, chain BB [auth J] SDF format, chain FA [auth D] SDF format, chain J [auth A] SDF format, chain NA [auth H] SDF format, chain NB [auth K] SDF format, chain Q [auth B] SDF format, chain UA [auth I] SDF format, chain Y [auth C] MOL2 format, chain BB [auth J] MOL2 format, chain FA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain NA [auth H] MOL2 format, chain NB [auth K] MOL2 format, chain Q [auth B] MOL2 format, chain UA [auth I] MOL2 format, chain Y [auth C] mmCIF format, chain BB [auth J] mmCIF format, chain FA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain NA [auth H] mmCIF format, chain NB [auth K] mmCIF format, chain Q [auth B] mmCIF format, chain UA [auth I] mmCIF format, chain Y [auth C]	BB [auth J] FA [auth D] J [auth A] NA [auth H] NB [auth K] BB [auth J], FA [auth D], J [auth A], NA [auth H], NB [auth K], Q [auth B], UA [auth I], Y [auth C]	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Interactions Focus chain BB [auth J] Focus chain FA [auth D] Focus chain J [auth A] Focus chain NA [auth H] Focus chain NB [auth K] Focus chain Q [auth B] Focus chain UA [auth I] Focus chain Y [auth C] Interactions & Density Focus chain BB [auth J] Focus chain FA [auth D] Focus chain J [auth A] Focus chain NA [auth H] Focus chain NB [auth K] Focus chain Q [auth B] Focus chain UA [auth I] Focus chain Y [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain GA [auth D] SDF format, chain GB [auth J] SDF format, chain HA [auth D] SDF format, chain HB [auth J] SDF format, chain IA [auth D] SDF format, chain IB [auth J] SDF format, chain JA [auth D] SDF format, chain JB [auth J] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain OA [auth H] SDF format, chain OB [auth K] SDF format, chain PA [auth H] SDF format, chain PB [auth K] SDF format, chain QA [auth H] SDF format, chain QB [auth K] SDF format, chain R [auth B] SDF format, chain RA [auth H] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain VA [auth I] SDF format, chain WA [auth I] SDF format, chain XA [auth I] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth J] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth J] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth J] MOL2 format, chain JA [auth D] MOL2 format, chain JB [auth J] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth H] MOL2 format, chain OB [auth K] MOL2 format, chain PA [auth H] MOL2 format, chain PB [auth K] MOL2 format, chain QA [auth H] MOL2 format, chain QB [auth K] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth H] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain VA [auth I] MOL2 format, chain WA [auth I] MOL2 format, chain XA [auth I] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain GB [auth J] mmCIF format, chain HA [auth D] mmCIF format, chain HB [auth J] mmCIF format, chain IA [auth D] mmCIF format, chain IB [auth J] mmCIF format, chain JA [auth D] mmCIF format, chain JB [auth J] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth H] mmCIF format, chain OB [auth K] mmCIF format, chain PA [auth H] mmCIF format, chain PB [auth K] mmCIF format, chain QA [auth H] mmCIF format, chain QB [auth K] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth H] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain VA [auth I] mmCIF format, chain WA [auth I] mmCIF format, chain XA [auth I] mmCIF format, chain Z [auth C]	AA [auth C] BA [auth C] CA [auth C] GA [auth D] GB [auth J] AA [auth C], BA [auth C], CA [auth C], GA [auth D], GB [auth J], HA [auth D], HB [auth J], IA [auth D], IB [auth J], JA [auth D], JB [auth J], K [auth A], L [auth A], M [auth A], N [auth A], OA [auth H], OB [auth K], PA [auth H], PB [auth K], QA [auth H], QB [auth K], R [auth B], RA [auth H], S [auth B], T [auth B], U [auth B], VA [auth I], WA [auth I], XA [auth I], Z [auth C]	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 GA [auth D] Focus chain GB [auth J] Focus chain HA [auth D] Focus chain HB [auth J] Focus chain IA [auth D] Focus chain IB [auth J] Focus chain JA [auth D] Focus chain JB [auth J] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth H] Focus chain OB [auth K] Focus chain PA [auth H] Focus chain PB [auth K] Focus chain QA [auth H] Focus chain QB [auth K] Focus chain R [auth B] Focus chain RA [auth H] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain VA [auth I] Focus chain WA [auth I] Focus chain XA [auth I] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain GA [auth D] Focus chain GB [auth J] Focus chain HA [auth D] Focus chain HB [auth J] Focus chain IA [auth D] Focus chain IB [auth J] Focus chain JA [auth D] Focus chain JB [auth J] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth H] Focus chain OB [auth K] Focus chain PA [auth H] Focus chain PB [auth K] Focus chain QA [auth H] Focus chain QB [auth K] Focus chain R [auth B] Focus chain RA [auth H] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain VA [auth I] Focus chain WA [auth I] Focus chain XA [auth I] Focus chain Z [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CB [auth J] SDF format, chain DB [auth J] SDF format, chain EB [auth J] SDF format, chain FB [auth J] MOL2 format, chain CB [auth J] MOL2 format, chain DB [auth J] MOL2 format, chain EB [auth J] MOL2 format, chain FB [auth J] mmCIF format, chain CB [auth J] mmCIF format, chain DB [auth J] mmCIF format, chain EB [auth J] mmCIF format, chain FB [auth J]	CB [auth J], DB [auth J], EB [auth J], FB [auth J]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CB [auth J] Focus chain DB [auth J] Focus chain EB [auth J] Focus chain FB [auth J] Interactions & Density Focus chain CB [auth J] Focus chain DB [auth J] Focus chain EB [auth J] Focus chain FB [auth J]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain KA [auth D] SDF format, chain KB [auth J] SDF format, chain O [auth A] SDF format, chain RB [auth K] SDF format, chain SA [auth H] SDF format, chain V [auth B] SDF format, chain YA [auth I] MOL2 format, chain DA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth J] MOL2 format, chain O [auth A] MOL2 format, chain RB [auth K] MOL2 format, chain SA [auth H] MOL2 format, chain V [auth B] MOL2 format, chain YA [auth I] mmCIF format, chain DA [auth C] mmCIF format, chain KA [auth D] mmCIF format, chain KB [auth J] mmCIF format, chain O [auth A] mmCIF format, chain RB [auth K] mmCIF format, chain SA [auth H] mmCIF format, chain V [auth B] mmCIF format, chain YA [auth I]	DA [auth C] KA [auth D] KB [auth J] O [auth A] RB [auth K] DA [auth C], KA [auth D], KB [auth J], O [auth A], RB [auth K], SA [auth H], V [auth B], YA [auth I]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain KA [auth D] Focus chain KB [auth J] Focus chain O [auth A] Focus chain RB [auth K] Focus chain SA [auth H] Focus chain V [auth B] Focus chain YA [auth I] Interactions & Density Focus chain DA [auth C] Focus chain KA [auth D] Focus chain KB [auth J] Focus chain O [auth A] Focus chain RB [auth K] Focus chain SA [auth H] Focus chain V [auth B] Focus chain YA [auth I]