Research workbench
The mature usutu saar-1776, model B
Analyse The mature usutu saar-1776, model B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LCH
- Type
- protein
- Length
- 1,711 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein E; Membrane protein M
- UniProt
- Q5WPU4, A0A0H3U5P6
- Ligands
- 0SM, PC7, NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Envelope protein E | protein | 495 | 24% helix, 36% strand | Q5WPU4 |
| B, D, F | Membrane protein M | protein | 75 | 57% helix, 0% strand | A0A0H3U5P6 |
| E | Envelope protein E | protein | 496 | 22% helix, 39% strand | Q5WPU4 |
Ligands and binding sites
- 0SM · Trimethyl-[2-[[(2S,3S)-2-(octadecanoylamino)-3-oxidanyl-butoxy]-oxidanyl-phosphoryl]oxyethyl]azanium · ligand · 3 copies · chains A, C, E
- PC7 · (7S)-4-hydroxy-N,N,N-trimethyl-9-oxo-7-[(palmitoyloxy) methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide · ligand · 3 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.84 | 0.85 | 123 | PC7 |
| 2 | 912 | 0.80 | 0.82 | 78 | PC7 |
| 3 | 991 | 0.76 | 0.79 | 109 | PC7 |
| 4 | 109 | 0.62 | 0.87 | 22 | empty |
| 5 | 122 | 0.61 | 0.85 | 23 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1608 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1594 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1580 Ų buried · 21 hydrogen bonds · protein-protein
- C–E · 1216 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 1100 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 6 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 7LCH · The mature Usutu SAAR-1776, Model B · the same entry in another collection · chain F against F, 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 Q5WPU4
- Every structure of UniProt A0A0H3U5P6
- Elsewhere: RCSB PDB 7LCH · PDBe 7LCH · UniProt Q5WPU4 · UniProt A0A0H3U5P6
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