MolNFT v1 · #135302 · protein
3D cryo-EM reconstruction of nucleotide-free msba in lipid nanodisc
5TV4 · Lipid a export ATP-BINDING/PERMEASE protein msba: “3D cryo-EM reconstruction of nucleotide-free msba in lipid nanodisc”. Electron microscopy, 7 ligands (FTT, PA1, MYR), 15 pockets (best druggability 0.80). MolNFT v1 #135302 on…
- PDB
- 5TV4
- Type
- protein
- Length
- 1,140 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipid a export ATP-BINDING/PERMEASE protein msba
- EC
- 3.6.3.-
- UniProt
- P60753
- Ligands
- FTT, PA1, MYR, DAO, GMH, KDO, PO4
- Pockets
- 15 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 62% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipid a export ATP-BINDING/PERMEASE protein msba (EC 3.6.3.-) | protein | 570 | 62% helix, 8% strand | P60753 |
Ligands and binding sites
- FTT · 3-hydroxy-tetradecanoic acid · ligand · 4 copies · chains B, A
- PA1 · 2-amino-2-deoxy-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- MYR · Myristic acid · ligand · chains B
- DAO · Lauric acid · ligand · chains B
- GMH · L-glycero-alpha-D-manno-heptopyranose · sugar · 3 copies · chains A
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 2 copies · chains B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.80 | 0.82 | 102 | empty |
| 2 | 470 | 0.80 | 0.87 | 74 | FTT |
| 3 | 825 | 0.80 | 0.83 | 102 | empty |
| 4 | 400 | 0.79 | 0.87 | 56 | empty |
| 5 | 587 | 0.78 | 0.84 | 97 | empty |
Interfaces
1 interface between chains.
- A–B · 2754 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5TV4 · 3D cryo-EM reconstruction of nucleotide-free MsbA in lipid nanodisc · the same entry in another collection · chain A against A, TM-score 1.00
- P60753 · AlphaFold monomer V2.0 prediction for ATP-dependent lipid a-core flippase (P60753) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P60753
- Elsewhere: RCSB PDB 5TV4 · PDBe 5TV4 · UniProt P60753
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