8RKY | pdb_00008rky

X-ray structure of the drug binding domain of AlbA in complex with the KMR-14-14 compound of the pyrrolobenzodiazepines class

PDB DOI: https://doi.org/10.2210/pdb8RKY/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Klebsiella oxytoca
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-01 Released: 2025-01-15
Deposition Author(s): Di Palma, M., Surani, Y.M., Rahman, K.M., Steiner, R.A.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Ministero dell Universita e della Ricerca

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.234 (Depositor), 0.235 (DCC)
R-Value Work:
0.208 (Depositor), 0.212 (DCC)

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

X-ray structure of the drug binding domain of AlbA in complex with the KMR-14-14 compound of the pyrrolobenzodiazepines class

Di Palma, M., Surani, Y.M., Rahman, K.M., Steiner, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 83.61 kDa
Atom Count: 6,088
Modeled Residue Count: 650
Deposited Residue Count: 672
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Albicidin resistance protein	A [auth BBB], B [auth CCC], C [auth AAA]	224	Klebsiella oxytoca	Mutation(s): 0 Gene Names: albA
UniProt
Find proteins for Q8KRS7 (Klebsiella oxytoca) Explore Q8KRS7 Go to UniProtKB: Q8KRS7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8KRS7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1H1Q (Subject of Investigation/LOI) Query on A1H1Q Download:Ideal Coordinates CCD File SDF format, chain H [auth CCC] SDF format, chain E [auth BBB] MOL2 format, chain H [auth CCC] MOL2 format, chain E [auth BBB] mmCIF format, chain H [auth CCC] mmCIF format, chain E [auth BBB]	E [auth BBB], H [auth CCC]	~{S}-[(2~{S},3~{S})-2,3-bis(oxidanyl)-4-sulfanyl-butyl] 4-[[5-[[4-[4-[[(6~{a}~{S})-2-methoxy-11-oxidanylidene-6~{a},7,8,9-tetrahydropyrrolo[2,1-c][1,4]benzodiazepin-3-yl]oxy]butanoylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-1-benzothiophen-2-yl]carbonylamino]-1-methyl-imidazole-2-carbothioate C₄₁ H₄₄ N₈ O₉ S₃ KAPRUVBCCMGSEO-UHFFFAOYSA-N		Interactions Focus chain E [auth BBB] Focus chain H [auth CCC] Interactions & Density Focus chain E [auth BBB] Focus chain H [auth CCC]
A1H1R (Subject of Investigation/LOI) Query on A1H1R Download:Ideal Coordinates CCD File SDF format, chain J [auth AAA] SDF format, chain I [auth AAA] SDF format, chain G [auth CCC] SDF format, chain D [auth BBB] MOL2 format, chain J [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain G [auth CCC] MOL2 format, chain D [auth BBB] mmCIF format, chain J [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain G [auth CCC] mmCIF format, chain D [auth BBB]	D [auth BBB], G [auth CCC], I [auth AAA], J [auth AAA]	ethyl 4-[[5-[[4-[4-[[(6~{a}~{S})-2-methoxy-11-oxidanylidene-6~{a},7,8,9-tetrahydropyrrolo[2,1-c][1,4]benzodiazepin-3-yl]oxy]butanoylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-1-benzothiophen-2-yl]carbonylamino]-1-methyl-imidazole-2-carboxylate C₃₉ H₄₀ N₈ O₈ S FOOOXHGRWPRUKF-RUZDIDTESA-N		Interactions Focus chain D [auth BBB] Focus chain G [auth CCC] Focus chain I [auth AAA] Focus chain J [auth AAA] Interactions & Density Focus chain D [auth BBB] Focus chain G [auth CCC] Focus chain I [auth AAA] Focus chain J [auth AAA]
DTV Query on DTV Download:Ideal Coordinates CCD File SDF format, chain L [auth AAA] SDF format, chain K [auth AAA] SDF format, chain F [auth BBB] MOL2 format, chain L [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain F [auth BBB] mmCIF format, chain L [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain F [auth BBB]	F [auth BBB], K [auth AAA], L [auth AAA]	(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-QWWZWVQMSA-N		Interactions Focus chain F [auth BBB] Focus chain K [auth AAA] Focus chain L [auth AAA] Interactions & Density Focus chain F [auth BBB] Focus chain K [auth AAA] Focus chain L [auth AAA]