AMP-pnp bound nanodisc reconstituted msba with nanobodies, spin- labeled at position T68C

Structure

electron microscopy · 2 distinct chains · 54% helix, 17% strand (DSSP).

Ligands and binding sites

• ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
• 88T · (1~{R},4~{R},11~{S},14~{S},19~{Z})-19-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylimino]-7,8,17, 18-tetraoxa-1,4,11,14-tetrazatricyclo[12.6.2.2^{4, 11}]tetracosane-6,9,16-trione · ligand · 2 copies · chains C, D
• MG · Magnesium ion · metal · 2 copies · chains A, B
• GD · Gadolinium atom · metal · 2 copies
• LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 7878 Ų buried · 54 hydrogen bonds · protein-protein
• B–C · 851 Ų buried · 14 hydrogen bonds · protein-protein
• A–D · 835 Ų buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).

Compared structures

• 7PH4 · AMP-PNP bound nanodisc reconstituted MsbA with nanobodies, spin-labeled at position T68C · the same entry in another collection · chain A against A, TM-score 1.00
• P60752 · AlphaFold monomer V2.0 prediction for ATP-dependent lipid a-core flippase (P60752) · a predicted model of the same protein · chain A against A, TM-score 0.71

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 P60752
• Elsewhere: RCSB PDB 7PH4 · PDBe 7PH4 · UniProt P60752