Research workbench
Putative osmotically inducible lipoprotein osme characterization by xray crystallography
Analyse Putative osmotically inducible lipoprotein osme characterization by xray… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DM5
- Type
- protein
- Length
- 356 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Osmotically inducible lipoprotein osme
- UniProt
- Q9HUT7
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Osmotically inducible lipoprotein osme | protein | 87 | 30% helix, 33% strand | Q9HUT7 |
| B | Osmotically inducible lipoprotein osme | protein | 95 | 28% helix, 31% strand | Q9HUT7 |
| D | Osmotically inducible lipoprotein osme | protein | 87 | 26% helix, 33% strand | Q9HUT7 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
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 | 208 | 0.48 | 0.75 | 34 | empty |
| 2 | 180 | 0.48 | 0.75 | 24 | empty |
| 3 | 66 | 0.30 | 0.74 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–C · 821 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 549 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 457 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 77 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 4DM5 · Putative Osmotically inducible lipoprotein OsmE characterization by Xray crystallography · 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 Q9HUT7
- Elsewhere: RCSB PDB 4DM5 · PDBe 4DM5 · UniProt Q9HUT7
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