Research workbench
Lolcde in complex with lipoprotein and amppnp complex undimerized form
Analyse Lolcde in complex with lipoprotein and amppnp complex undimerized form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ARJ
- Type
- protein
- Length
- 1,262 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
- ANP, Z41, PLM, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 33% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Lipoprotein-releasing ABC transporter permease subunit lolc | protein | 392 | 37% helix, 15% strand | A0A4S5ATA9 |
| E | Lipoprotein-releasing system transmembrane protein lole | protein | 409 | 44% helix, 13% strand | P75958 |
| F | Lipoprotein-releasing system ATP-binding protein lold (EC 7.6.2.-) | protein | 225 | 28% helix, 13% strand | P75957 |
| D | Lipoprotein-releasing system ATP-binding protein lold (EC 7.6.2.-) | protein | 226 | 13% helix, 14% strand | P75957 |
| V | Lpp | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains E, F, 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, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.83 | 0.83 | 71 | Z41, PLM |
| 2 | 978 | 0.75 | 0.78 | 76 | empty |
| 3 | 81 | 0.72 | 0.95 | 19 | empty |
| 4 | 276 | 0.68 | 0.83 | 37 | empty |
| 5 | 63 | 0.68 | 0.95 | 20 | empty |
Interfaces
7 interfaces between chains.
- C–E · 2443 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1198 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 1078 Ų buried · 6 hydrogen bonds · protein-protein
- E–V · 360 Ų buried · 1 hydrogen bond · protein-protein
- C–V · 211 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 lipid (covalent ligand, palmitoylation).
Compared structures
- 7ARJ · LolCDE in complex with lipoprotein and AMPPNP complex undimerized form · 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 0.93
- 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 7ARJ · PDBe 7ARJ · UniProt A0A4S5ATA9 · UniProt P75958 · UniProt P75957
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