Research workbench
Structure of a membrane protein
Analyse Structure of a membrane protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q35
- Type
- protein
- Length
- 908 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.393
- Source
- Shigella flexneri
- Molecule
- LPS-assembly protein LptD; LPS-assembly lipoprotein LptE
- UniProt
- Q83SQ0, Q83LX4
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.393 · 2 distinct chains · 11% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LPS-assembly protein LptD | protein | 758 | 6% helix, 57% strand | Q83SQ0 |
| B | LPS-assembly lipoprotein LptE | protein | 150 | 35% helix, 35% strand | Q83LX4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
- LDA · Lauryl dimethylamine-N-oxide · additive · 7 copies · chains A
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.84 | 0.92 | 67 | SO4 |
| 2 | 627 | 0.83 | 0.89 | 74 | empty |
| 3 | 817 | 0.83 | 0.86 | 74 | C8E, LDA |
| 4 | 751 | 0.81 | 0.84 | 93 | empty |
| 5 | 248 | 0.79 | 0.92 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 3519 Ų buried · 51 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4Q35 · Structure of a membrane protein · the same entry in another collection · chain A against A, TM-score 1.00
- Q83LX4 · AlphaFold monomer V2.0 prediction for lps-assembly lipoprotein lpte (Q83LX4) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q83SQ0 · AlphaFold monomer V2.0 prediction for lps-assembly protein lptd (Q83SQ0) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q83SQ0
- Every structure of UniProt Q83LX4
- Elsewhere: RCSB PDB 4Q35 · PDBe 4Q35 · UniProt Q83SQ0 · UniProt Q83LX4
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