MolNFT v1 · #173714 · protein

Levofloxacin bound structure of bacterial efflux pump.

7B8T · Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump…: “Levofloxacin bound structure of bacterial efflux pump.”. X-ray diffraction, 1 ligand (LFX), 20 pockets (best druggability 0.87). MolNFT v1 #173714 on GenesisL1: 3D…

PDB: 7B8T
Type: protein
Length: 2,204 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb; Darpin
UniProt: P31224
Ligands: LFX
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 5 distinct chains · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb	protein	578	32% helix, 35% strand	P31224
C	Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb	protein	572	34% helix, 32% strand	P31224
D	Darpin	protein	160	52% helix, 1% strand	—
E	Darpin	protein	155	54% helix, 0% strand	—
F	Darpin	protein	161	53% helix, 0% strand	—

Ligands and binding sites

LFX · (3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid · ligand · chains C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	999	0.87	0.89	106	empty
2	1163	0.87	0.89	128	empty
3	863	0.85	0.88	102	empty
4	1143	0.85	0.86	129	empty
5	942	0.84	0.85	79	LFX

Interfaces

9 interfaces between chains.

B–C · 3106 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 3027 Å² buried · 33 hydrogen bonds · protein-protein
A–C · 2657 Å² buried · 31 hydrogen bonds · protein-protein
C–E · 909 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 865 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

7B8T · Levofloxacin bound structure of bacterial efflux pump. · the same entry in another collection · chain F against F, TM-score 1.00
P31224 · AlphaFold monomer V2.0 prediction for multidrug efflux pump subunit acrb (P31224) · a predicted model of the same protein · chain A against A, TM-score 0.94

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P31224
Elsewhere: RCSB PDB 7B8T · PDBe 7B8T · UniProt P31224

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