MolNFT v1 · #173187 · protein
Lolcde in complex with lipoprotein and lola
7ARM · Lipoprotein-releasing ABC transporter permease subunit lolc: “Lolcde in complex with lipoprotein and lola”. Electron microscopy, 2 ligands (Z41, PLM), 20 pockets (best druggability 0.82). MolNFT v1 #173187 on GenesisL1: 3D…
- PDB
- 7ARM
- Type
- protein
- Length
- 1,438 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein-releasing ABC transporter permease subunit lolc; Lipoprotein-releasing system…
- EC
- 7.6.2.-
- UniProt
- A0A4S5ATA9, P75958, P75957, P61316
- Ligands
- Z41, PLM
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 31% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Lipoprotein-releasing ABC transporter permease subunit lolc | protein | 392 | 39% helix, 16% strand | A0A4S5ATA9 |
| E | Lipoprotein-releasing system transmembrane protein lole | protein | 409 | 42% helix, 13% strand | P75958 |
| F | Lipoprotein-releasing system ATP-binding protein lold (EC 7.6.2.-) | protein | 221 | 24% helix, 11% strand | P75957 |
| D | Lipoprotein-releasing system ATP-binding protein lold (EC 7.6.2.-) | protein | 224 | 24% helix, 7% strand | P75957 |
| V | Lpp | protein | 10 | 0% helix, 0% strand | — |
| A | Outer-membrane lipoprotein carrier protein | protein | 182 | 7% helix, 31% strand | P61316 |
Ligands and binding sites
- Z41 · (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate · ligand · chains C, E, V
- PLM · Palmitic acid · ligand · chains C, E, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.82 | 0.86 | 59 | Z41, PLM |
| 2 | 1082 | 0.81 | 0.82 | 94 | empty |
| 3 | 217 | 0.79 | 0.92 | 43 | empty |
| 4 | 136 | 0.77 | 0.94 | 39 | empty |
| 5 | 436 | 0.72 | 0.83 | 50 | empty |
Interfaces
8 interfaces between chains.
- C–E · 2372 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1338 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1041 Ų buried · 3 hydrogen bonds · protein-protein
- C–A · 874 Ų buried · 8 hydrogen bonds · protein-protein
- E–V · 367 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 lipid (covalent ligand, palmitoylation).
Compared structures
- 7ARM · LolCDE in complex with lipoprotein and LolA · the same entry in another collection · chain A against A, TM-score 1.00
- P75958 · AlphaFold monomer V2.0 prediction for lipoprotein-releasing system transmembrane protein… · a predicted model of the same protein · chain E against A, TM-score 0.93
- P75957 · AlphaFold monomer V2.0 prediction for lipoprotein-releasing system ATP-binding protein… · a predicted model of the same protein · chain F against A, TM-score 0.91
- P61316 · AlphaFold monomer V2.0 prediction for outer-membrane lipoprotein carrier protein (P61316) · 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 A0A4S5ATA9
- Every structure of UniProt P75958
- Every structure of UniProt P75957
- Every structure of UniProt P61316
- Elsewhere: RCSB PDB 7ARM · PDBe 7ARM · UniProt A0A4S5ATA9 · UniProt P75958 · UniProt P75957 · UniProt P61316
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.