Research workbench
LOLCD(E171Q)E with bound amppnp in nanodiscs
Analyse LOLCD(E171Q)E with bound amppnp in nanodiscs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V8I
- Type
- protein
- Length
- 1,261 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein-releasing system transmembrane protein lolc; Lipoprotein-releasing system…
- EC
- 7.6.2.-
- UniProt
- P0ADC3, P75957, P75958
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Lipoprotein-releasing system transmembrane protein lolc | protein | 396 | 43% helix, 18% strand | P0ADC3 |
| D, F | Lipoprotein-releasing system ATP-binding protein lold (EC 7.6.2.-) | protein | 229 | 35% helix, 24% strand | P75957 |
| E | Lipoprotein-releasing system transmembrane protein lole | protein | 407 | 48% helix, 10% strand | P75958 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains C, D, F
- MG · Magnesium ion · metal · 2 copies · chains D, F
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 | 1106 | 0.85 | 0.86 | 99 | empty |
| 2 | 610 | 0.82 | 0.87 | 92 | empty |
| 3 | 572 | 0.80 | 0.85 | 62 | empty |
| 4 | 405 | 0.76 | 0.86 | 46 | MG, ANP |
| 5 | 307 | 0.72 | 0.85 | 40 | MG, ANP |
Interfaces
6 interfaces between chains.
- C–E · 2512 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1387 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1342 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1023 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 146 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7V8I · LolCD(E171Q)E with bound AMPPNP in nanodiscs · the same entry in another collection · chain C against C, 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 D against A, TM-score 0.89
- P0ADC3 · AlphaFold monomer V2.0 prediction for lipoprotein-releasing system transmembrane protein… · a predicted model of the same protein · chain C against A, TM-score 0.82
- 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 0.69
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 P0ADC3
- Every structure of UniProt P75957
- Every structure of UniProt P75958
- Elsewhere: RCSB PDB 7V8I · PDBe 7V8I · UniProt P0ADC3 · UniProt P75957 · UniProt P75958
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