8B5D

Exploring the ligand binding and conformational dynamics of receptor domain 1 of the ABC transporter GlnPQ

PDB DOI: https://doi.org/10.2210/pdb8B5D/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Lactococcus lactis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-09-22 Released: 2023-10-04
Deposition Author(s): Whittaker, J., Guskov, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.263
R-Value Work: 0.197
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6H30

Literature

Exploring the ligand binding and conformational dynamics of receptor domain 1 of the ABC transporter GlnPQ

Whittaker, J., Guskov, A.

To be published.

Macromolecule Content

Total Structure Weight: 49.99 kDa
Atom Count: 3,702
Modelled Residue Count: 446
Deposited Residue Count: 450
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter permease subunit	A, B	225	Lactococcus lactis	Mutation(s): 0 Gene Names: glnP, AMHIJAGA_02474, GII02_01815
UniProt
Find proteins for A0A2X0R690 (Lactococcus lactis) Explore A0A2X0R690 Go to UniProtKB: A0A2X0R690
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2X0R690
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLN (Subject of Investigation/LOI) Query on GLN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B]	F [auth A], L [auth B]	GLUTAMINE C₅ H₁₀ N₂ O₃ ZDXPYRJPNDTMRX-VKHMYHEASA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B]	D [auth A], E [auth A], I [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	G [auth A], H [auth A], M [auth B], N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B]