Research workbench
Lolcde in complex with lipoprotein
Analyse Lolcde in complex with lipoprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ARH
- Type
- protein
- Length
- 1,261 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
- Z41, PLM
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Lipoprotein-releasing ABC transporter permease subunit lolc | protein | 392 | 40% helix, 16% strand | A0A4S5ATA9 |
| E | Lipoprotein-releasing system transmembrane protein lole | protein | 409 | 38% helix, 13% strand | P75958 |
| F, D | Lipoprotein-releasing system ATP-binding protein lold (EC 7.6.2.-) | protein | 225 | 26% helix, 18% strand | P75957 |
| V | Lpp | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- Z41 · (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate · ligand · chains C, E, V
- PLM · Palmitic acid · ligand · chains 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.84 | 0.85 | 74 | Z41, PLM |
| 2 | 119 | 0.77 | 0.95 | 23 | empty |
| 3 | 117 | 0.76 | 0.95 | 30 | empty |
| 4 | 421 | 0.74 | 0.84 | 49 | empty |
| 5 | 84 | 0.70 | 0.94 | 27 | empty |
Interfaces
7 interfaces between chains.
- C–E · 2359 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1399 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1100 Ų buried · 4 hydrogen bonds · protein-protein
- E–V · 347 Ų buried · 4 hydrogen bonds · protein-protein
- C–V · 182 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 lipid (covalent ligand, palmitoylation).
Compared structures
- 7ARH · LolCDE in complex with lipoprotein · the same entry in another collection · chain E against E, 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 0.92
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 7ARH · PDBe 7ARH · UniProt A0A4S5ATA9 · UniProt P75958 · UniProt P75957
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