MolNFT v1 · #125375 · protein
A protein structure
5L75 · Lipopolysaccharide ABC transporter, ATP-binding protein lptb: “A protein structure”. X-ray diffraction, 1 ligand (PT), 13 pockets (best druggability 0.75). MolNFT v1 #125375 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5L75
- Type
- protein
- Length
- 1,135 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipopolysaccharide ABC transporter, ATP-binding protein lptb; FIG000988: predicted…
- UniProt
- W1B6A5, W1B830, W1B8C5
- Ligands
- PT
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipopolysaccharide ABC transporter, ATP-binding protein lptb | protein | 235 | 34% helix, 19% strand | W1B6A5 |
| B | Lipopolysaccharide ABC transporter, ATP-binding protein lptb | protein | 237 | 30% helix, 24% strand | W1B6A5 |
| F | FIG000988: predicted permease | protein | 323 | 51% helix, 7% strand | W1B830 |
| G | FIG000906: predicted permease | protein | 340 | 50% helix, 7% strand | W1B8C5 |
Ligands and binding sites
- PT · Platinum (II) ion · metal · 2 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.75 | 0.81 | 70 | empty |
| 2 | 908 | 0.73 | 0.77 | 68 | empty |
| 3 | 624 | 0.71 | 0.79 | 62 | empty |
| 4 | 476 | 0.67 | 0.78 | 58 | empty |
| 5 | 458 | 0.65 | 0.78 | 48 | empty |
Interfaces
4 interfaces between chains.
- F–G · 1812 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 1016 Ų buried · 9 hydrogen bonds · protein-protein
- A–G · 996 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 618 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5L75 · A protein structure · 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 W1B6A5
- Every structure of UniProt W1B830
- Every structure of UniProt W1B8C5
- Elsewhere: RCSB PDB 5L75 · PDBe 5L75 · UniProt W1B6A5 · UniProt W1B830 · UniProt W1B8C5
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