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Cryo-EM structure of P.AERUGINOSA mlafebd

Analyse Cryo-EM structure of P.AERUGINOSA mlafebd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7CH9
Type: protein
Length: 2,126 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mlad domain-containing protein; Probable permease of ABC transporter; Probable…
UniProt: Q9HVW3, Q9HVW2, Q9HVW1, Q9HVW5
Ligands: LPP
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 7 distinct chains · 48% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mlad domain-containing protein	protein	150	18% helix, 31% strand	Q9HVW3
B, C, D, F	Mlad domain-containing protein	protein	148	20% helix, 27% strand	Q9HVW3
E	Mlad domain-containing protein	protein	149	19% helix, 29% strand	Q9HVW3
G	Probable permease of ABC transporter	protein	258	79% helix, 0% strand	Q9HVW2
H	Probable permease of ABC transporter	protein	257	80% helix, 0% strand	Q9HVW2
I, J	Probable ATP-binding component of ABC transporter	protein	262	38% helix, 20% strand	Q9HVW1
K, L	Stas domain-containing protein	protein	98	40% helix, 15% strand	Q9HVW5

Ligands and binding sites

LPP · 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate · ligand · 10 copies · chains A, B, C, F, D, E, G, H

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	502	0.81	0.87	55	LPP
2	652	0.78	0.84	100	empty
3	874	0.71	0.76	117	empty
4	68	0.71	0.96	21	empty
5	646	0.66	0.75	56	LPP

Interfaces

32 interfaces between chains.

I–J · 2022 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 2019 Å² buried · 16 hydrogen bonds · protein-protein
B–H · 1039 Å² buried · 3 hydrogen bonds · protein-protein
G–I · 980 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 946 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

7CH9 · Cryo-EM structure of P.aeruginosa MlaFEBD · the same entry in another collection · chain A against A, 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 Q9HVW3
Every structure of UniProt Q9HVW2
Every structure of UniProt Q9HVW1
Every structure of UniProt Q9HVW5
Elsewhere: RCSB PDB 7CH9 · PDBe 7CH9 · UniProt Q9HVW3 · UniProt Q9HVW2 · UniProt Q9HVW1 · UniProt Q9HVW5

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