MolNFT v1 · #117960 · protein

MBX3135 bound structure of bacterial efflux pump.

5ENR · Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump…: “MBX3135 bound structure of bacterial efflux pump.”. X-ray diffraction, 1 ligand (MBX), 20 pockets (best druggability 0.88). MolNFT v1 #117960 on GenesisL1: 3D structure…

PDB: 5ENR
Type: protein
Length: 2,216 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: MBX
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	34% helix, 35% 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	156	53% helix, 0% strand	—

Ligands and binding sites

MBX · ~{N}-[4-[2-[[5-cyano-8-[(2~{S},6~{S})-2,6-dimethylmorpholin-4-yl]-3,3-dimethyl-1,4-dihydropyrano[3,4-c]pyridin-6-yl]sulfanyl]ethyl]phenyl]prop-2-enamide · 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	914	0.88	0.90	115	empty
2	1158	0.87	0.89	122	empty
3	1086	0.85	0.86	94	MBX
4	601	0.82	0.87	47	empty
5	525	0.81	0.87	46	empty

Interfaces

9 interfaces between chains.

B–C · 3177 Å² buried · 43 hydrogen bonds · protein-protein
A–B · 3027 Å² buried · 34 hydrogen bonds · protein-protein
A–C · 2671 Å² buried · 28 hydrogen bonds · protein-protein
C–E · 926 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 916 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5ENR · MBX3135 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 5ENR · PDBe 5ENR · UniProt P31224

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