MolNFT v1 · #185162 · protein
AMP-pnp bound nanodisc reconstituted msba with nanobodies, spin- labeled at position A60C
7PH3 · ATP-dependent lipid a-core flippase: “AMP-pnp bound nanodisc reconstituted msba with nanobodies, spin- labeled at position A60C”. Electron microscopy, 5 ligands (ANP, 3PE, 88T), 20 pockets (best druggability 0.89). MolNFT v1 #185162…
- PDB
- 7PH3
- Type
- protein
- Length
- 1,380 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent lipid a-core flippase; Nanobody NB_MSBA#1
- EC
- 7.5.2.6
- UniProt
- P60752
- Ligands
- ANP, 3PE, 88T, MG, GD
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 2 distinct chains · 53% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-dependent lipid a-core flippase (EC 7.5.2.6) | protein | 577 | 62% helix, 10% strand | P60752 |
| C, D | Nanobody NB_MSBA#1 | protein | 113 | 5% helix, 50% strand | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · 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 B, C, A, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.89 | 0.91 | 121 | ANP, MG |
| 2 | 611 | 0.88 | 0.94 | 92 | empty |
| 3 | 367 | 0.85 | 0.94 | 62 | empty |
| 4 | 181 | 0.73 | 0.90 | 33 | ANP, MG |
| 5 | 315 | 0.69 | 0.83 | 52 | empty |
Interfaces
3 interfaces between chains.
- A–B · 7994 Ų buried · 67 hydrogen bonds · protein-protein
- B–C · 862 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 857 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 7PH3 · AMP-PNP bound nanodisc reconstituted MsbA 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 0.71
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 7PH3 · PDBe 7PH3 · UniProt P60752
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