Research workbench

Cryo-EM structure of mlafedb in complex with AMP-pnp

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

PDB: 6ZY9
Type: protein
Length: 1,985 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: ANP, MG
Pockets: 20 · best druggability 0.78

Structure

electron microscopy · 12 distinct chains · 35% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yrbd protein	protein	132	20% helix, 22% strand	D6IEA5
D	Yrbd protein	protein	108	15% helix, 31% strand	D6IEA5
I	Yrbd protein	protein	131	17% helix, 31% strand	D6IEA5
J	Yrbd protein	protein	136	24% helix, 23% strand	D6IEA5
K	Yrbd protein	protein	127	18% helix, 35% strand	D6IEA5
L	Yrbd protein	protein	129	19% helix, 26% strand	D6IEA5
B	ABC transporter maintaining om lipid asymmetry, cytoplasmic stas component	protein	93	24% helix, 18% strand	W8T4U6
C	ABC transporter maintaining om lipid asymmetry, cytoplasmic stas component	protein	96	26% helix, 8% strand	W8T4U6
F	Toluene tolerance protein TTG2A	protein	258	25% helix, 12% strand	V0AC37
G	Toluene tolerance protein TTG2A	protein	260	27% helix, 12% strand	V0AC37
E	Uncharacterized protein	protein	256	68% helix, 0% strand	I2X585
H	Uncharacterized protein	protein	259	72% helix, 0% strand	I2X585

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · 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	139	0.78	0.95	34	empty
2	123	0.76	0.95	25	empty
3	480	0.76	0.84	40	empty
4	891	0.75	0.78	76	empty
5	106	0.73	0.93	29	empty

Interfaces

23 interfaces between chains.

E–H · 1985 Å² buried · 4 hydrogen bonds · protein-protein
F–G · 1762 Å² buried · 15 hydrogen bonds · protein-protein
A–H · 953 Å² buried · 6 hydrogen bonds · protein-protein
F–E · 924 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 914 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6ZY9 · Cryo-EM structure of MlaFEDB in complex with AMP-PNP · 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 6ZY9 · PDBe 6ZY9 · UniProt D6IEA5 · UniProt W8T4U6 · UniProt V0AC37 · UniProt I2X585

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