Research workbench
Nanodisc reconstituted msba in complex with nanobodies, spin-labeled at position A60C
Analyse Nanodisc reconstituted msba in complex with nanobodies, spin-labeled at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PH2
- Type
- protein
- Length
- 1,362 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent lipid a-core flippase; NB_MSBA#1
- EC
- 7.5.2.6
- UniProt
- P60752
- Ligands
- 88T, EIW, GD
- Pockets
- 16 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-dependent lipid a-core flippase (EC 7.5.2.6) | protein | 569 | 57% helix, 6% strand | P60752 |
| C | NB_MSBA#1 | protein | 111 | 3% helix, 48% strand | — |
| D | NB_MSBA#1 | protein | 113 | 3% helix, 49% strand | — |
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 B, C, A, 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
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.83 | 0.83 | 102 | EIW |
| 2 | 275 | 0.62 | 0.80 | 40 | empty |
| 3 | 342 | 0.60 | 0.77 | 50 | empty |
| 4 | 366 | 0.60 | 0.76 | 35 | empty |
| 5 | 321 | 0.59 | 0.77 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 5339 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 889 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 887 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 109 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 100 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 7PH2 · Nanodisc reconstituted MsbA in complex with nanobodies, spin-labeled at position A60C · 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 0.90
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 7PH2 · PDBe 7PH2 · UniProt P60752
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