Research workbench

Cryo-EM structure of mlafedb in complex with phospholipid

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

PDB: 6ZY3
Type: protein
Length: 2,071 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yrbd protein; ABC transporter maintaining om lipid asymmetry, cytoplasmic stas component…
UniProt: D6IEA5, W8T4U6, V0AC37, I2X585
Ligands: PEE
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 12 distinct chains · 34% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yrbd protein	protein	144	22% helix, 27% strand	D6IEA5
D	Yrbd protein	protein	131	24% helix, 18% strand	D6IEA5
I	Yrbd protein	protein	135	23% helix, 19% strand	D6IEA5
J	Yrbd protein	protein	144	22% helix, 25% strand	D6IEA5
K	Yrbd protein	protein	145	12% helix, 30% strand	D6IEA5
L	Yrbd protein	protein	140	15% helix, 31% strand	D6IEA5
B	ABC transporter maintaining om lipid asymmetry, cytoplasmic stas component	protein	98	31% helix, 15% strand	W8T4U6
C	ABC transporter maintaining om lipid asymmetry, cytoplasmic stas component	protein	95	28% helix, 15% strand	W8T4U6
F	Toluene tolerance protein TTG2A	protein	261	28% helix, 15% strand	V0AC37
G	Toluene tolerance protein TTG2A	protein	262	31% helix, 12% strand	V0AC37
E	Uncharacterized protein	protein	258	61% helix, 0% strand	I2X585
H	Uncharacterized protein	protein	258	67% helix, 0% strand	I2X585

Ligands and binding sites

PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · chains K, E, 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, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	656	0.85	0.89	54	PEE
2	437	0.78	0.87	69	empty
3	153	0.78	0.94	27	empty
4	589	0.77	0.84	49	empty
5	688	0.77	0.82	90	empty

Interfaces

27 interfaces between chains.

F–G · 2031 Å² buried · 19 hydrogen bonds · protein-protein
E–H · 1783 Å² buried · 2 hydrogen bonds · protein-protein
J–K · 973 Å² buried · 8 hydrogen bonds · protein-protein
J–E · 952 Å² buried · 2 hydrogen bonds · protein-protein
G–H · 928 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6ZY3 · Cryo-EM structure of MlaFEDB in complex with phospholipid · 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 D6IEA5
Every structure of UniProt W8T4U6
Every structure of UniProt V0AC37
Every structure of UniProt I2X585
Elsewhere: RCSB PDB 6ZY3 · PDBe 6ZY3 · UniProt D6IEA5 · UniProt W8T4U6 · UniProt V0AC37 · UniProt I2X585

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