MolNFT v1 · #152583 · protein
Cryo-EM structure of an alphavirus, sindbis virus
6IMM · Spike glycoprotein E1: “Cryo-EM structure of an alphavirus, sindbis virus”. Electron microscopy, 1 ligand (8K6), 20 pockets (best druggability 0.82). MolNFT v1 #152583 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IMM
- Type
- protein
- Length
- 3,180 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein E1; Spike glycoprotein E2; Assembly protein E3
- Ligands
- 8K6
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 12% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N, T, Z, a | Spike glycoprotein E1 | protein | 423 | 9% helix, 28% strand | — |
| P, V, d, e | Spike glycoprotein E2 | protein | 325 | 12% helix, 28% strand | — |
| R, X, h, i | Assembly protein E3 | protein | 47 | 32% helix, 4% strand | — |
Ligands and binding sites
- 8K6 · Octadecane · ligand · chains Z, d
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.82 | 0.84 | 87 | empty |
| 2 | 1010 | 0.80 | 0.81 | 77 | empty |
| 3 | 712 | 0.79 | 0.84 | 60 | empty |
| 4 | 875 | 0.73 | 0.78 | 69 | empty |
| 5 | 364 | 0.71 | 0.82 | 51 | empty |
Interfaces
16 interfaces between chains.
- a–e · 3040 Ų buried · 29 hydrogen bonds · protein-protein
- Z–d · 2975 Ų buried · 29 hydrogen bonds · protein-protein
- T–V · 2880 Ų buried · 28 hydrogen bonds · protein-protein
- N–P · 2746 Ų buried · 22 hydrogen bonds · protein-protein
- P–R · 510 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6IMM · Cryo-EM structure of an alphavirus, 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
- Elsewhere: RCSB PDB 6IMM · PDBe 6IMM
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