MolNFT v1 · #123514 · protein

Fusidic acid bound acrb

5JMN · Multidrug efflux pump subunit acrb: “Fusidic acid bound acrb”. X-ray diffraction, 7 ligands (PTY, D12, FUA), 20 pockets (best druggability 0.87). MolNFT v1 #123514 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JMN
Type: protein
Length: 3,413 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Multidrug efflux pump subunit acrb; Darpin
UniProt: P31224
Ligands: PTY, D12, FUA, ETE, D10, P3G, SO4
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 54% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Multidrug efflux pump subunit acrb	protein	1034	54% helix, 20% strand	P31224
C	Multidrug efflux pump subunit acrb	protein	1033	55% helix, 20% strand	P31224
D	Darpin	protein	158	54% helix, 0% strand	—
E	Darpin	protein	154	54% helix, 0% strand	—

Ligands and binding sites

PTY · Phosphatidylethanolamine · ligand · 4 copies · chains A, B, C
D12 · Dodecane · ligand · 4 copies · chains B, C, A
FUA · Fusidic acid · ligand · 3 copies · chains A, B, C
ETE · 2-{2-[2-2-(methoxy-ethoxy)-ethoxy]-ethoxy}-ethanol · ligand · 3 copies · chains A, C
D10 · Decane · ligand · 2 copies · chains B, A
P3G · 3,6,9,12,15-pentaoxaheptadecane · ligand · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, C
LMT · Dodecyl-beta-D-maltoside · additive · 10 copies · chains A, C, B
GOL · Glycerol · additive · 8 copies · chains A, E, B, C, D
HEX · Hexane · additive · 2 copies · chains A, B, C
OCT · N-octane · additive · 2 copies · chains B, 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	724	0.87	0.91	88	SO4
2	916	0.87	0.89	102	empty
3	781	0.86	0.88	105	empty
4	1193	0.85	0.86	127	GOL
5	608	0.82	0.87	51	GOL

Interfaces

7 interfaces between chains.

A–B · 3596 Å² buried · 49 hydrogen bonds · protein-protein
A–C · 3361 Å² buried · 37 hydrogen bonds · protein-protein
B–C · 3098 Å² buried · 31 hydrogen bonds · protein-protein
A–E · 848 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 847 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5JMN · Fusidic acid bound AcrB · the same entry in another collection · chain E against E, 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 C against A, TM-score 0.99

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 5JMN · PDBe 5JMN · UniProt P31224

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