Research workbench
Mapping the E2 glycoprotein of alphaviruses
Analyse Mapping the E2 glycoprotein of alphaviruses in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z8Y
- Type
- protein
- Length
- 2,388 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein E1; Spike glycoprotein E2; Capsid protein C
- EC
- 3.4.21.-
- UniProt
- P03316, P11259
- Pockets
- 19 · best druggability 0.61
Structure
electron microscopy · 5 distinct chains · 11% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Spike glycoprotein E1 | protein | 290 | 6% helix, 31% strand | P03316 |
| B, D, F, H | Spike glycoprotein E1 | protein | 89 | 0% helix, 31% strand | P03316 |
| I, K, M, O | Spike glycoprotein E1 | protein | 31 | 26% helix, 0% strand | P03316 |
| J, L, N, P | Spike glycoprotein E2 | protein | 36 | 86% helix, 0% strand | P11259 |
| Q, R, S, T | Capsid protein C (EC 3.4.21.-) | protein | 151 | 6% helix, 48% strand | P03316 |
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.61 | 0.93 | 25 | empty |
| 2 | 88 | 0.57 | 0.86 | 19 | empty |
| 3 | 236 | 0.56 | 0.78 | 41 | empty |
| 4 | 141 | 0.53 | 0.81 | 27 | empty |
| 5 | 93 | 0.51 | 0.83 | 22 | empty |
Interfaces
19 interfaces between chains.
- C–D · 566 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 523 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 456 Ų buried · 9 hydrogen bonds · protein-protein
- M–N · 408 Ų buried · 0 hydrogen bonds · protein-protein
- K–L · 407 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 1Z8Y · Mapping the E2 Glycoprotein of Alphaviruses · the same entry in another collection · chain J against J, 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 P11259
- Elsewhere: RCSB PDB 1Z8Y · PDBe 1Z8Y · UniProt P03316 · UniProt P11259
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.