MolNFT v1 · #161131 · protein

Fusidic acid bound ACRB_V340A

6Q4N · Multidrug efflux pump subunit acrb: “Fusidic acid bound ACRB_V340A”. X-ray diffraction, 7 ligands (D10, PTY, FUA), 20 pockets (best druggability 0.88). MolNFT v1 #161131 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6Q4N
Type: protein
Length: 3,414 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: D10, PTY, FUA, DDQ, DDR, D12, SO4
Pockets: 20 · best druggability 0.88

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Multidrug efflux pump subunit acrb	protein	1036	53% helix, 20% strand	P31224
B, C	Multidrug efflux pump subunit acrb	protein	1034	55% helix, 19% strand	P31224
D	Darpin	protein	156	54% helix, 0% strand	—
E	Darpin	protein	154	55% helix, 0% strand	—

Ligands and binding sites

D10 · Decane · ligand · 5 copies · chains B, A, C
PTY · Phosphatidylethanolamine · ligand · 4 copies · chains B, C
FUA · Fusidic acid · ligand · 3 copies · chains A, B, C
DDQ · Decylamine-N,N-dimethyl-N-oxide · ligand · 2 copies · chains B, C
DDR · (2S)-3-hydroxypropane-1,2-diyl didecanoate · ligand · chains B
D12 · Dodecane · ligand · chains B
SO4 · Sulfate ion · ion · 2 copies · chains B, C
LMT · Dodecyl-beta-D-maltoside · additive · 8 copies · chains A, C, B
GOL · Glycerol · additive · 6 copies · chains A, C, B, E
OCT · N-octane · additive · 5 copies · chains B, C, A
HEX · Hexane · additive · 2 copies · chains B, C
P6G · Hexaethylene glycol · additive · chains A

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	985	0.88	0.89	125	empty
2	719	0.87	0.91	82	GOL
3	1137	0.85	0.87	119	GOL
4	935	0.85	0.87	124	empty
5	527	0.84	0.90	62	empty

Interfaces

7 interfaces between chains.

A–B · 3636 Å² buried · 40 hydrogen bonds · protein-protein
A–C · 3439 Å² buried · 36 hydrogen bonds · protein-protein
B–C · 3109 Å² buried · 31 hydrogen bonds · protein-protein
B–D · 888 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 840 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6Q4N · Fusidic acid bound AcrB_V340A · 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 6Q4N · PDBe 6Q4N · UniProt P31224

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.