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Cryo-EM structure of mlafedb in nanodiscs with phospholipid substrates

Analyse Cryo-EM structure of mlafedb in nanodiscs with phospholipid substrates in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XBD
Type: protein
Length: 2,404 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phospholipid ABC transporter-binding protein mlad; Phospholipid ABC transporter permease…
EC: 3.6.3.-
UniProt: H4UPP8, H4UPP9, H4UPQ0, H4UPP6
Ligands: PEF
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 12 distinct chains · 52% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phospholipid ABC transporter-binding protein mlad	protein	144	22% helix, 30% strand	H4UPP8
B	Phospholipid ABC transporter-binding protein mlad	protein	138	20% helix, 32% strand	H4UPP8
C	Phospholipid ABC transporter-binding protein mlad	protein	144	22% helix, 28% strand	H4UPP8
D	Phospholipid ABC transporter-binding protein mlad	protein	143	22% helix, 30% strand	H4UPP8
E	Phospholipid ABC transporter-binding protein mlad	protein	145	24% helix, 29% strand	H4UPP8
F	Phospholipid ABC transporter-binding protein mlad	protein	143	22% helix, 26% strand	H4UPP8
G	Phospholipid ABC transporter permease protein mlae	protein	256	85% helix, 0% strand	H4UPP9
H	Phospholipid ABC transporter permease protein mlae	protein	255	86% helix, 0% strand	H4UPP9
I, J	Phospholipid transport system ATP-binding protein mlaf (EC 3.6.3.-)	protein	263	36% helix, 21% strand	H4UPQ0
K, L	Phospholipid ABC transporter-binding protein mlab	protein	95	35% helix, 15% strand	H4UPP6
M	MSP1D1	protein	164	99% helix, 0% strand	—
N	MSP1D1	protein	156	98% helix, 0% strand	—

Ligands and binding sites

PEF · Di-palmitoyl-3-sn-phosphatidylethanolamine · ligand · 2 copies · chains A, B, C, D, E, F, 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	926	0.87	0.88	101	PEF
2	514	0.79	0.86	50	empty
3	451	0.76	0.85	70	empty
4	319	0.74	0.86	47	empty
5	780	0.70	0.76	69	empty

Interfaces

44 interfaces between chains.

I–J · 2041 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 1768 Å² buried · 4 hydrogen bonds · protein-protein
A–F · 1050 Å² buried · 5 hydrogen bonds · protein-protein
A–G · 998 Å² buried · 0 hydrogen bonds · protein-protein
D–H · 971 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6XBD · Cryo-EM structure of MlaFEDB in nanodiscs with phospholipid substrates · 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 H4UPP8
Every structure of UniProt H4UPP9
Every structure of UniProt H4UPQ0
Every structure of UniProt H4UPP6
Elsewhere: RCSB PDB 6XBD · PDBe 6XBD · UniProt H4UPP8 · UniProt H4UPP9 · UniProt H4UPQ0 · UniProt H4UPP6

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