Research workbench
Lolcde in complex with lipoprotein and ADP
Analyse Lolcde in complex with lipoprotein and ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ARL
- Type
- protein
- Length
- 1,256 residues
- Chains
- 5
- 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
- Ligands
- ADP, Z41, PLM, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 34% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Lipoprotein-releasing ABC transporter permease subunit lolc | protein | 392 | 40% helix, 14% strand | A0A4S5ATA9 |
| E | Lipoprotein-releasing system transmembrane protein lole | protein | 409 | 38% helix, 11% strand | P75958 |
| F | Lipoprotein-releasing system ATP-binding protein lold (EC 7.6.2.-) | protein | 223 | 28% helix, 18% strand | P75957 |
| D | Lipoprotein-releasing system ATP-binding protein lold (EC 7.6.2.-) | protein | 222 | 22% helix, 16% strand | P75957 |
| V | Lpp | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains E, F, C, D
- Z41 · (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate · ligand · chains C, E, V
- PLM · Palmitic acid · ligand · chains E, V
- MG · Magnesium ion · metal · 2 copies · chains F, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.84 | 0.86 | 73 | Z41, PLM |
| 2 | 84 | 0.74 | 0.96 | 19 | empty |
| 3 | 106 | 0.72 | 0.93 | 32 | empty |
| 4 | 328 | 0.70 | 0.83 | 45 | empty |
| 5 | 309 | 0.66 | 0.81 | 33 | empty |
Interfaces
6 interfaces between chains.
- C–E · 2507 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1356 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 1053 Ų buried · 4 hydrogen bonds · protein-protein
- E–V · 345 Ų buried · 2 hydrogen bonds · protein-protein
- C–V · 218 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 lipid (covalent ligand, palmitoylation).
Compared structures
- 7ARL · LolCDE in complex with lipoprotein and ADP · the same entry in another collection · chain V against V, TM-score 1.00
- 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 0.94
- 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
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
- Elsewhere: RCSB PDB 7ARL · PDBe 7ARL · UniProt A0A4S5ATA9 · UniProt P75958 · UniProt P75957
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