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Cryo-EM structure of multidrug efflux pump mexab-oprm (0 degree state)

Analyse Cryo-EM structure of multidrug efflux pump mexab-oprm (0 degree state) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IOK
Type: protein
Length: 6,441 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Multidrug resistance protein mexa; Outer membrane protein oprm; Multidrug resistance…
UniProt: P52477, Q51487, P52002
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 7 distinct chains · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I	Multidrug resistance protein mexa	protein	329	21% helix, 35% strand	P52477
J	Multidrug resistance protein mexa	protein	333	20% helix, 36% strand	P52477
K, M	Multidrug resistance protein mexa	protein	331	18% helix, 34% strand	P52477
L, N	Multidrug resistance protein mexa	protein	334	19% helix, 37% strand	P52477
A, B, C	Outer membrane protein oprm	protein	455	58% helix, 11% strand	Q51487
F	Multidrug resistance protein mexb	protein	1024	50% helix, 17% strand	P52002
G, E	Multidrug resistance protein mexb	protein	1030	50% helix, 16% strand	P52002

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	1187	0.90	0.92	135	empty
2	684	0.87	0.92	79	empty
3	253	0.81	0.93	45	empty
4	1019	0.81	0.82	108	empty
5	738	0.81	0.84	71	empty

Interfaces

33 interfaces between chains.

F–G · 3726 Å² buried · 39 hydrogen bonds · protein-protein
F–E · 3461 Å² buried · 32 hydrogen bonds · protein-protein
G–E · 3453 Å² buried · 39 hydrogen bonds · protein-protein
A–C · 2640 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 2605 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

6IOK · Cryo-EM structure of multidrug efflux pump MexAB-OprM (0 degree state) · the same entry in another collection · chain E against E, 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 P52477
Every structure of UniProt Q51487
Every structure of UniProt P52002
Elsewhere: RCSB PDB 6IOK · PDBe 6IOK · UniProt P52477 · UniProt Q51487 · UniProt P52002

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