8YKS | pdb_00008yks

PaThiL in complex with AMP-PNP

PDB DOI: https://doi.org/10.2210/pdb8YKS/pdb
Entry: 8YKS supersedes: 7DU3

Classification: PROTEIN BINDING
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-05 Released: 2025-03-12
Deposition Author(s): Lin, J.Q., Chung, Z., Lescar, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.198 (Depositor), 0.199 (DCC)
R-Value Work:
0.182 (Depositor), 0.184 (DCC)
R-Value Observed:
0.183 (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

ThiL in complex with AMP-PNP

Lin, J.Q., Lescar, J.

To be published.

Macromolecule Content

Total Structure Weight: 72.59 kDa
Atom Count: 5,145
Modeled Residue Count: 639
Deposited Residue Count: 688
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamine-monophosphate kinase	A [auth B], B [auth A]	344	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: thiL, CAZ10_30480, DY930_26150, FDK04_05055, IPC116_27470, IPC1323_04495, IPC1509_03965, IPC582_16370, IPC620_29520, NCTC13621_06786 EC: 2.7.4.16
UniProt
Find proteins for Q9HWX7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HWX7 Go to UniProtKB: Q9HWX7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HWX7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain O [auth A] MOL2 format, chain H [auth B] MOL2 format, chain O [auth A] mmCIF format, chain H [auth B] mmCIF format, chain O [auth A]	H [auth B], O [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain H [auth B] Focus chain O [auth A] Interactions & Density Focus chain H [auth B] Focus chain O [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	C [auth B] D [auth B] E [auth B] J [auth A] K [auth A] C [auth B], D [auth B], E [auth B], J [auth A], K [auth A], L [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	F [auth B], G [auth B], M [auth A], N [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain M [auth A] Focus chain N [auth A]