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Cryo-EM structure of mlafedb in complex with ADP

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

PDB: 6ZY4
Type: protein
Length: 1,978 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: ADP, MG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 10 distinct chains · 26% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yrbd protein	protein	135	24% helix, 27% strand	D6IEA5
D	Yrbd protein	protein	105	9% helix, 43% strand	D6IEA5
I	Yrbd protein	protein	134	19% helix, 30% strand	D6IEA5
J	Yrbd protein	protein	136	20% helix, 29% strand	D6IEA5
K	Yrbd protein	protein	107	8% helix, 32% strand	D6IEA5
L	Yrbd protein	protein	128	16% helix, 30% strand	D6IEA5
B	ABC transporter maintaining om lipid asymmetry, cytoplasmic stas component	protein	95	14% helix, 8% strand	W8T4U6
C	ABC transporter maintaining om lipid asymmetry, cytoplasmic stas component	protein	96	13% helix, 6% strand	W8T4U6
F, G	Toluene tolerance protein TTG2A	protein	262	26% helix, 11% strand	V0AC37
E, H	Uncharacterized protein	protein	259	63% helix, 0% strand	I2X585

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains F, G
MG · Magnesium ion · metal · 2 copies · chains F, G

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	856	0.86	0.88	59	empty
2	643	0.77	0.82	103	empty
3	733	0.75	0.80	84	empty
4	233	0.73	0.87	34	empty
5	127	0.72	0.92	27	empty

Interfaces

28 interfaces between chains.

F–G · 1990 Å² buried · 14 hydrogen bonds · protein-protein
E–H · 1946 Å² buried · 1 hydrogen bond · protein-protein
A–H · 910 Å² buried · 5 hydrogen bonds · protein-protein
F–E · 884 Å² buried · 7 hydrogen bonds · protein-protein
J–K · 877 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6ZY4 · Cryo-EM structure of MlaFEDB in complex with ADP · 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 6ZY4 · PDBe 6ZY4 · UniProt D6IEA5 · UniProt W8T4U6 · UniProt V0AC37 · UniProt I2X585

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