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Cryo-EM structure of apo mlafedb

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

PDB: 6ZY2
Type: protein
Length: 2,091 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
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 10 distinct chains · 29% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yrbd protein	protein	149	22% helix, 23% strand	D6IEA5
D, J	Yrbd protein	protein	144	19% helix, 23% strand	D6IEA5
I	Yrbd protein	protein	136	17% helix, 25% strand	D6IEA5
K	Yrbd protein	protein	146	16% helix, 23% strand	D6IEA5
L	Yrbd protein	protein	140	15% helix, 25% strand	D6IEA5
B	ABC transporter maintaining om lipid asymmetry, cytoplasmic stas component	protein	95	34% helix, 22% strand	W8T4U6
C	ABC transporter maintaining om lipid asymmetry, cytoplasmic stas component	protein	96	29% helix, 13% strand	W8T4U6
F	Toluene tolerance protein TTG2A	protein	261	26% helix, 14% strand	V0AC37
G	Toluene tolerance protein TTG2A	protein	262	28% helix, 14% strand	V0AC37
E, H	Uncharacterized protein	protein	259	63% helix, 0% strand	I2X585

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	1110	0.87	0.88	116	empty
2	687	0.78	0.83	73	empty
3	367	0.76	0.86	71	empty
4	99	0.75	0.96	26	empty
5	122	0.73	0.93	30	empty

Interfaces

29 interfaces between chains.

E–H · 1966 Å² buried · 5 hydrogen bonds · protein-protein
F–G · 1890 Å² buried · 17 hydrogen bonds · protein-protein
A–H · 1004 Å² buried · 6 hydrogen bonds · protein-protein
J–K · 972 Å² buried · 5 hydrogen bonds · protein-protein
J–E · 964 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6ZY2 · Cryo-EM structure of apo MlaFEDB · 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 D6IEA5
Every structure of UniProt W8T4U6
Every structure of UniProt V0AC37
Every structure of UniProt I2X585
Elsewhere: RCSB PDB 6ZY2 · PDBe 6ZY2 · UniProt D6IEA5 · UniProt W8T4U6 · UniProt V0AC37 · UniProt I2X585

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