MolNFT v1 · #180299 · protein
Structure of west nile virus (kunjin)
7KVA · Envelope protein E: “Structure of west nile virus (kunjin)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.84). MolNFT v1 #180299 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KVA
- Type
- protein
- Length
- 1,716 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein E; Matrix protein M
- UniProt
- A0A0U2IWM5, A0A0A6ZKT6
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 27% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Envelope protein E | protein | 501 | 23% helix, 39% strand | A0A0U2IWM5 |
| a, b, c | Matrix protein M | protein | 71 | 51% helix, 0% strand | A0A0A6ZKT6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.84 | 0.87 | 64 | empty |
| 2 | 986 | 0.78 | 0.80 | 102 | empty |
| 3 | 365 | 0.76 | 0.86 | 59 | empty |
| 4 | 328 | 0.75 | 0.87 | 56 | empty |
| 5 | 98 | 0.62 | 0.88 | 18 | empty |
Interfaces
9 interfaces between chains.
- C–c · 1444 Ų buried · 14 hydrogen bonds · protein-protein
- A–a · 1442 Ų buried · 13 hydrogen bonds · protein-protein
- B–b · 1424 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1251 Ų buried · 9 hydrogen bonds · protein-protein
- a–b · 978 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7KVA · Structure of West Nile virus (Kunjin) · 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 A0A0U2IWM5
- Every structure of UniProt A0A0A6ZKT6
- Elsewhere: RCSB PDB 7KVA · PDBe 7KVA · UniProt A0A0U2IWM5 · UniProt A0A0A6ZKT6
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