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Fusidic acid bound ACRB_I27A

Analyse Fusidic acid bound ACRB_I27A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Q4O
Type: protein
Length: 3,421 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: DDQ, D10, D12, PTY, FUA, DDR, SO4
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 5 distinct chains · 55% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Multidrug efflux pump subunit acrb	protein	1042	54% helix, 20% strand	P31224
B	Multidrug efflux pump subunit acrb	protein	1034	55% helix, 19% strand	P31224
C	Multidrug efflux pump subunit acrb	protein	1035	55% helix, 20% strand	P31224
D	Darpin	protein	156	54% helix, 0% strand	—
E	Darpin	protein	154	55% helix, 0% strand	—

Ligands and binding sites

DDQ · Decylamine-N,N-dimethyl-N-oxide · ligand · 9 copies · chains A, C, B
D10 · Decane · ligand · 8 copies · chains A, B, C
D12 · Dodecane · ligand · 4 copies · chains B, A, C
PTY · Phosphatidylethanolamine · ligand · 4 copies · chains B, C, A
FUA · Fusidic acid · ligand · chains B
DDR · (2S)-3-hydroxypropane-1,2-diyl didecanoate · ligand · chains B
SO4 · Sulfate ion · ion · chains C
GOL · Glycerol · additive · 11 copies · chains A, C, E, B, D
HEX · Hexane · additive · 9 copies · chains A, B, C
LMT · Dodecyl-beta-D-maltoside · additive · 8 copies · chains A, C, B
OCT · N-octane · additive · 4 copies · chains A, B

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	812	0.88	0.91	98	GOL
2	979	0.87	0.89	125	empty
3	1087	0.86	0.88	129	empty
4	901	0.85	0.87	95	empty
5	496	0.83	0.89	47	GOL

Interfaces

7 interfaces between chains.

A–B · 3666 Å² buried · 46 hydrogen bonds · protein-protein
A–C · 3367 Å² buried · 43 hydrogen bonds · protein-protein
B–C · 3132 Å² buried · 32 hydrogen bonds · protein-protein
B–D · 961 Å² buried · 11 hydrogen bonds · protein-protein
A–E · 929 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6Q4O · Fusidic acid bound AcrB_I27A · 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 6Q4O · PDBe 6Q4O · UniProt P31224

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