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Apo structure of bacterial efflux pump.

Analyse Apo structure of bacterial efflux pump. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EN5
Type: protein
Length: 2,221 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
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 6 distinct chains · 37% helix, 27% 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	584	32% helix, 32% strand	P31224
D	Darpin	protein	161	52% helix, 1% strand	—
E	Darpin	protein	156	53% helix, 0% strand	—
F	Darpin	protein	162	52% helix, 0% strand	—

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	904	0.88	0.91	124	empty
2	963	0.87	0.89	109	empty
3	1135	0.85	0.86	104	empty
4	832	0.84	0.86	87	empty
5	1029	0.83	0.84	97	empty

Interfaces

9 interfaces between chains.

B–C · 3114 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 3017 Å² buried · 37 hydrogen bonds · protein-protein
A–C · 2651 Å² buried · 27 hydrogen bonds · protein-protein
C–E · 918 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 862 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5EN5 · Apo 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 5EN5 · PDBe 5EN5 · UniProt P31224

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