9CS5 | pdb_00009cs5

E. Coli AMTB with bound Xe ions

PDB DOI: https://doi.org/10.2210/pdb9CS5/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-07-23 Released: 2025-07-30
Deposition Author(s): Vahedi-Faridi, A., Kowatz, T., Lodowski, D.T.
Funding Organization(s): Office of Naval Research (ONR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.174 (Depositor), 0.181 (DCC)
R-Value Work:
0.152 (Depositor), 0.164 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

E. Coli AMTB with bound Xe ions

Vahedi-Faridi, A., Kowatz, T., Lodowski, D.T.

To be published.

Macromolecule Content

Total Structure Weight: 48.59 kDa
Atom Count: 2,952
Modeled Residue Count: 372
Deposited Residue Count: 446
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ammonium transporter AmtB	A	446	Escherichia coli K-12	Mutation(s): 0 Gene Names: amtB, ybaG, b0451, JW0441
UniProt
Find proteins for P69681 (Escherichia coli (strain K12)) Explore P69681 Go to UniProtKB: P69681
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69681
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
XE (Subject of Investigation/LOI) Query on XE Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A]	O [auth A], P [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain O [auth A] Focus chain P [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NH2 Query on NH2 Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A]	Q [auth A], R [auth A]	AMINO GROUP H₂ N QGZKDVFQNNGYKY-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A]