MolNFT v1 · #117959 · protein

MBX3132 bound structure of bacterial efflux pump.

5ENQ · Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump…: “MBX3132 bound structure of bacterial efflux pump.”. X-ray diffraction, 1 ligand (5QE), 20 pockets (best druggability 0.88). MolNFT v1 #117959 on GenesisL1: 3D structure…

PDB: 5ENQ
Type: protein
Length: 2,215 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb; Darpin
UniProt: P31224
Ligands: 5QE
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 5 distinct chains · 36% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb	protein	580	33% helix, 36% strand	P31224
B	Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb	protein	578	33% helix, 36% strand	P31224
C	Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb	protein	578	33% helix, 33% strand	P31224
D, F	Darpin	protein	162	52% helix, 0% strand	—
E	Darpin	protein	155	53% helix, 0% strand	—

Ligands and binding sites

5QE · ~{N}-[4-[2-[[5-cyano-8-[(2~{S},6~{R})-2,6-dimethylmorpholin-4-yl]-3,3-dimethyl-1,4-dihydropyrano[3,4-c]pyridin-6-yl]sulfanyl]ethyl]phenyl]ethanamide · ligand · 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, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	821	0.88	0.91	113	empty
2	1162	0.87	0.89	128	empty
3	687	0.86	0.90	131	empty
4	909	0.84	0.86	95	empty
5	742	0.83	0.87	82	empty

Interfaces

9 interfaces between chains.

B–C · 3118 Å² buried · 38 hydrogen bonds · protein-protein
A–B · 2990 Å² buried · 37 hydrogen bonds · protein-protein
A–C · 2683 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 886 Å² buried · 9 hydrogen bonds · protein-protein
C–E · 877 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5ENQ · MBX3132 bound structure of bacterial efflux pump. · the same entry in another collection · chain F against F, 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 A against A, TM-score 0.94

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 5ENQ · PDBe 5ENQ · UniProt P31224

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