MolNFT v1 · #105845 · protein
Crystal structure of the outer membrane lipopolysaccharide transport protein lpte (rlpb) from escherichia COLI in the tetragonal crystal form
4RH8 · Lps-assembly lipoprotein lpte: “Crystal structure of the outer membrane lipopolysaccharide transport protein lpte (rlpb) from escherichia…”. X-ray diffraction, 11 pockets (best druggability 0.85). MolNFT v1 #105845 on GenesisL1: 3D…
- PDB
- 4RH8
- Type
- protein
- Length
- 534 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lps-assembly lipoprotein lpte
- UniProt
- P0ADC1
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Lps-assembly lipoprotein lpte | protein | 133 | 32% helix, 42% strand | P0ADC1 |
| C | Lps-assembly lipoprotein lpte | protein | 135 | 31% helix, 40% strand | P0ADC1 |
Ligands and binding sites
- FMT · Formic acid · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.85 | 0.88 | 54 | empty |
| 2 | 273 | 0.68 | 0.84 | 38 | empty |
| 3 | 299 | 0.66 | 0.82 | 40 | empty |
| 4 | 442 | 0.62 | 0.76 | 44 | empty |
| 5 | 339 | 0.56 | 0.75 | 37 | empty |
Interfaces
6 interfaces between chains.
- B–C · 925 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 874 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 853 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 836 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 54 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4RH8 · Crystal structure of the outer membrane lipopolysaccharide transport protein LptE (RlpB)… · the same entry in another collection · chain A against A, TM-score 1.00
- P0ADC1 · AlphaFold monomer V2.0 prediction for lps-assembly lipoprotein lpte (P0ADC1) · a predicted model of the same protein · chain A 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 P0ADC1
- Elsewhere: RCSB PDB 4RH8 · PDBe 4RH8 · UniProt P0ADC1
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