Research workbench
OmpUdeltaN (N-terminus deletion mutant of OmpU), outer membrane protein of Vibrio cholerae
Analyse OmpUdeltaN (N-terminus deletion mutant of OmpU), outer membrane protein of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EHC
- Type
- protein
- Length
- 614 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.02
- Source
- Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
- Molecule
- Outer membrane protein U
- UniProt
- A5F934
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · resolution 2.02 · 1 distinct chain · 4% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Outer membrane protein U | protein | 307 | 4% helix, 64% strand | A5F934 |
Ligands and binding sites
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.47 | 0.74 | 45 | empty |
| 2 | 146 | 0.39 | 0.74 | 26 | empty |
| 3 | 67 | 0.26 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 72 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6EHC · Ompudeltan (N-terminus deletion mutant of ompu), outer membrane protein of vibrio cholerae · the same entry in another collection · chain A against A, TM-score 1.00
- A5F934 · AlphaFold monomer V2.0 prediction for outer membrane protein U (A5F934) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 A5F934
- Elsewhere: RCSB PDB 6EHC · PDBe 6EHC · UniProt A5F934
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