Nanodisc reconstituted msba in complex with nanobodies, spin-labeled at position T68C

Structure

electron microscopy · 3 distinct chains · 41% helix, 20% strand (DSSP).

Ligands and binding sites

• 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
• EIW · (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl) ethyl]-4-[(2~{R},3~{S},4~{S},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{S},5~{S}, 6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,5-bis(oxidanyl)oxan-2-yl]oxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-4-[(3~{R})-3-nonanoyloxytetradecanoyl]oxy-5-[[(3~{R})-3-octanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S}, 4~{S},5~{S},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanylnonanoyl]amino]-4-[(3~{R})-3-oxidanylt · ligand · chains A, B
• GD · Gadolinium atom · metal · 2 copies

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 5542 Ų buried · 27 hydrogen bonds · protein-protein
• A–D · 901 Ų buried · 9 hydrogen bonds · protein-protein
• B–C · 884 Ų buried · 7 hydrogen bonds · protein-protein
• A–C · 110 Ų buried · 0 hydrogen bonds · protein-protein
• B–D · 109 Ų buried · 1 hydrogen bond · protein-protein

Modifications

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

Compared structures

• 7PH7 · Nanodisc reconstituted MsbA in complex with nanobodies, spin-labeled at position T68C · 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 C3TGA2
• Elsewhere: RCSB PDB 7PH7 · PDBe 7PH7 · UniProt C3TGA2