Research workbench
Cryo-EM structure of the multiple peptide resistance factor (mprf) loaded with one lysyl-phosphatidylglycerol molecule
Analyse Cryo-EM structure of the multiple peptide resistance factor (mprf) loaded with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LVF
- Type
- protein
- Length
- 1,586 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low pH-inducible protein lpia
- UniProt
- L0LM43
- Ligands
- EV9, LHG, PGT
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Low pH-inducible protein lpia | protein | 793 | 56% helix, 8% strand | L0LM43 |
Ligands and binding sites
- EV9 · [(2~{R})-3-[[(2~{S})-3-[(2~{S})-2,6-bis(azanyl) hexanoyl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-2-hexadecanoyloxy-propyl] hexadecanoate · ligand · 2 copies · chains B, A
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 2 copies · chains B, A
- PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.86 | 0.86 | 92 | LHG, PGT |
| 2 | 1094 | 0.85 | 0.86 | 111 | EV9 |
| 3 | 1107 | 0.85 | 0.86 | 113 | EV9 |
| 4 | 766 | 0.81 | 0.84 | 75 | empty |
| 5 | 848 | 0.81 | 0.83 | 77 | empty |
Interfaces
1 interface between chains.
- B–A · 732 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6LVF · Cryo-EM structure of the multiple peptide resistance factor (MprF) loaded with one… · the same entry in another collection · chain B against B, 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 L0LM43
- Elsewhere: RCSB PDB 6LVF · PDBe 6LVF · UniProt L0LM43
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