MolNFT v1 · #172008 · protein

Minocycline binding to the deep binding pocket of acrb-G619P

6ZO6 · Multidrug efflux pump subunit acrb: “Minocycline binding to the deep binding pocket of acrb-G619P”. X-ray diffraction, 13 ligands (DDQ, D10, D12), 20 pockets (best druggability 0.88). MolNFT v1 #172008 on GenesisL1: 3D structure…

PDB: 6ZO6
Type: protein
Length: 3,419 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, MYS, MIY, DDR, 8K6, R16, C14, PTY, LPX, CL, SO4
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 5 distinct chains · 54% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Multidrug efflux pump subunit acrb	protein	1042	54% helix, 19% strand	P31224
B	Multidrug efflux pump subunit acrb	protein	1033	55% helix, 20% strand	P31224
C	Multidrug efflux pump subunit acrb	protein	1034	54% helix, 19% 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 · 5 copies · chains A, B, C
D10 · Decane · ligand · 5 copies · chains B, C, A
D12 · Dodecane · ligand · 3 copies · chains A, C
MYS · Pentadecane · ligand · 2 copies · chains A, B
MIY · (4s,4as,5ar,12as)-4,7-bis(dimethylamino)-3,10,12,12A-tetrahydroxy-1,11-dioxo-1,4,4A,5,5A,6,11,12A-octahydrotetracene-2-carboxamide · ligand · chains B
DDR · (2S)-3-hydroxypropane-1,2-diyl didecanoate · ligand · chains B
8K6 · Octadecane · ligand · chains A, B
R16 · Hexadecane · ligand · chains B, C
C14 · Tetradecane · ligand · chains C
PTY · Phosphatidylethanolamine · ligand · chains B, C
LPX · (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate · ligand · chains C
CL · Chloride ion · ion · 3 copies · chains B, C
SO4 · Sulfate ion · ion · chains B
EDO · 1,2-ethanediol · additive · 24 copies · chains A, B, D, C
GOL · Glycerol · additive · 14 copies · chains A, C, B, E
LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, C, B
HEX · Hexane · additive · 6 copies · chains A, B, C
OCT · N-octane · additive · 3 copies · chains A, C
PGE · Triethylene glycol · additive · 2 copies · chains A, B, C
PG4 · Tetraethylene glycol · additive · chains A, B, C
1PE · Pentaethylene glycol · additive · 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	896	0.88	0.90	92	GOL, EDO
2	648	0.85	0.90	77	EDO
3	803	0.85	0.88	74	empty
4	1058	0.83	0.84	100	empty
5	602	0.83	0.88	86	MIY, EDO

Interfaces

7 interfaces between chains.

A–B · 3601 Å² buried · 43 hydrogen bonds · protein-protein
A–C · 3397 Å² buried · 37 hydrogen bonds · protein-protein
B–C · 3094 Å² buried · 40 hydrogen bonds · protein-protein
B–D · 850 Å² buried · 10 hydrogen bonds · protein-protein
A–E · 848 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6ZO6 · Minocycline binding to the deep binding pocket of AcrB-G619P · 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 6ZO6 · PDBe 6ZO6 · UniProt P31224

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