Research workbench
Cryo-EM structure of LPTB2FGC in complex with AMP-pnp
Analyse Cryo-EM structure of LPTB2FGC in complex with AMP-pnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S8G
- Type
- protein
- Length
- 957 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipopolysaccharide ABC transporter, ATP-binding protein lptb; Lps export ABC transporter…
- UniProt
- E7T9E6, A0A1W2MGV2, A0A2S4N3I3
- Ligands
- ANP, LMD
- Pockets
- 8 · best druggability 0.89
Structure
electron microscopy · 4 distinct chains · 40% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipopolysaccharide ABC transporter, ATP-binding protein lptb | protein | 238 | 26% helix, 19% strand | E7T9E6 |
| B | Lipopolysaccharide ABC transporter, ATP-binding protein lptb | protein | 239 | 26% helix, 19% strand | E7T9E6 |
| F | Lps export ABC transporter permease lptf | protein | 236 | 50% helix, 0% strand | A0A1W2MGV2 |
| G | Inner membrane protein yjgq | protein | 244 | 57% helix, 1% strand | A0A2S4N3I3 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B, G, F
- LMD · tetradecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside · ligand · chains F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.89 | 0.91 | 128 | ANP, LMD |
| 2 | 1162 | 0.77 | 0.79 | 102 | empty |
| 3 | 289 | 0.73 | 0.86 | 38 | empty |
| 4 | 392 | 0.67 | 0.80 | 44 | ANP |
| 5 | 174 | 0.51 | 0.78 | 28 | empty |
Interfaces
6 interfaces between chains.
- F–G · 1527 Ų buried · 1 hydrogen bond · protein-protein
- A–G · 1267 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 1094 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 979 Ų buried · 10 hydrogen bonds · protein-protein
- B–G · 186 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6S8G · Cryo-EM structure of LptB2FGC in complex with AMP-PNP · the same entry in another collection · chain A against A, TM-score 1.00
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 E7T9E6
- Every structure of UniProt A0A1W2MGV2
- Every structure of UniProt A0A2S4N3I3
- Elsewhere: RCSB PDB 6S8G · PDBe 6S8G · UniProt E7T9E6 · UniProt A0A1W2MGV2 · UniProt A0A2S4N3I3
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