Research workbench
Crystal structure of the outer membrane lipopolysaccharide transport protein lpte (rlpb) from escherichia COLI in the tetragonal crystal form
Analyse Crystal structure of the outer membrane lipopolysaccharide transport protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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