Research workbench
Placement of the structural proteins in sindbis virus
Analyse Placement of the structural proteins in sindbis virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LD4
- Type
- protein
- Length
- 2,304 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein C; General control protein GCN4; Spike glycoprotein E1
- EC
- 3.4.21.-
- UniProt
- P03316, P03069
- Ligands
- UNX
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · 3 distinct chains · 2% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Coat protein C (EC 3.4.21.-) | protein | 151 | 6% helix, 48% strand | P03316 |
| E, F, G, H, I, J, K, L | General control protein GCN4 | protein | 28 | 0% helix, 0% strand | P03069 |
| M, N, O, P | Spike glycoprotein E1 | protein | 369 | 1% helix, 22% strand | P03316 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 32 copies · chains N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.73 | 0.91 | 42 | empty |
| 2 | 166 | 0.72 | 0.90 | 43 | empty |
| 3 | 157 | 0.71 | 0.90 | 35 | empty |
| 4 | 156 | 0.71 | 0.90 | 41 | empty |
| 5 | 213 | 0.56 | 0.79 | 25 | empty |
Interfaces
7 interfaces between chains.
- M–N · 365 Ų buried · 6 hydrogen bonds · protein-protein
- M–O · 185 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 181 Ų buried · 0 hydrogen bonds · protein-protein
- K–L · 36 Ų buried · 0 hydrogen bonds · protein-protein
- G–H · 36 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1LD4 · Placement of the Structural Proteins in Sindbis Virus · the same entry in another collection · chain N against N, 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 P03316
- Every structure of UniProt P03069
- Elsewhere: RCSB PDB 1LD4 · PDBe 1LD4 · UniProt P03316 · UniProt P03069
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