Research workbench

Multi-drug efflux; membrane transport; rnd superfamily; drug resistance

Analyse Multi-drug efflux; membrane transport; rnd superfamily; drug resistance in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NG5
Type: protein
Length: 6,569 residues
Chains: 15
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Multidrug efflux pump subunit acra; Outer membrane protein tolc; Multidrug efflux pump…
UniProt: P0AE06, P02930, P31224, P0AAW9
Ligands: 5QF
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 5 distinct chains · 44% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, D, G, H, A, B	Multidrug efflux pump subunit acra	protein	340	21% helix, 22% strand	P0AE06
F, I, C	Outer membrane protein tolc	protein	428	64% helix, 17% strand	P02930
K, L	Multidrug efflux pump subunit acrb	protein	1037	42% helix, 15% strand	P31224
M, N, O	Multidrug efflux pump accessory protein acrz	protein	46	50% helix, 0% strand	P0AAW9
J	Multidrug efflux pump subunit acrb	protein	1033	45% helix, 13% strand	P31224

Ligands and binding sites

5QF · 6-[2-(3,4-dimethoxyphenyl)ethylsulfanyl]-8-[4-(2-methoxyethyl)piperazin-1-yl]-3,3-dimethyl-1,4-dihydropyrano[3,4-c]pyridine-5-carbonitrile · ligand · 3 copies · chains K, L, J

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	1169	0.89	0.91	150	5QF
2	1094	0.89	0.91	135	5QF
3	433	0.85	0.93	70	empty
4	331	0.82	0.92	53	5QF
5	217	0.79	0.92	30	empty

Interfaces

36 interfaces between chains.

L–J · 3816 Å² buried · 55 hydrogen bonds · protein-protein
K–L · 3769 Å² buried · 49 hydrogen bonds · protein-protein
K–J · 3652 Å² buried · 43 hydrogen bonds · protein-protein
I–C · 2444 Å² buried · 49 hydrogen bonds · protein-protein
F–C · 2431 Å² buried · 49 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent (covalent ligand).

Compared structures

5NG5 · multi-drug efflux; membrane transport; RND superfamily; Drug resistance · the same entry in another collection · chain L against L, TM-score 1.00

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 P0AE06
Every structure of UniProt P02930
Every structure of UniProt P31224
Every structure of UniProt P0AAW9
Elsewhere: RCSB PDB 5NG5 · PDBe 5NG5 · UniProt P0AE06 · UniProt P02930 · UniProt P31224 · UniProt P0AAW9

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