MolNFT v1 · #189129 · protein
DENV2_NGC_FAB_C10 28DEGREE (1FAB:3E)
7V3F · Envelope protein E: “DENV2_NGC_FAB_C10 28DEGREE (1FAB:3E)”. Electron microscopy, 1 ligand (NAG), 19 pockets (best druggability 0.83). MolNFT v1 #189129 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7V3F
- Type
- protein
- Length
- 1,701 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein E; Small envelope protein M
- UniProt
- P14340
- Ligands
- NAG
- Pockets
- 19 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Envelope protein E | protein | 495 | 16% helix, 36% strand | P14340 |
| E, D, F | Small envelope protein M | protein | 72 | 51% helix, 1% strand | P14340 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.83 | 0.84 | 96 | empty |
| 2 | 1066 | 0.78 | 0.79 | 96 | empty |
| 3 | 925 | 0.77 | 0.80 | 88 | empty |
| 4 | 765 | 0.72 | 0.78 | 66 | empty |
| 5 | 444 | 0.62 | 0.76 | 62 | empty |
Interfaces
9 interfaces between chains.
- A–D · 1752 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 1740 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 1709 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1635 Ų buried · 14 hydrogen bonds · protein-protein
- B–A · 1320 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan (N-glycosylation).
Compared structures
- 7V3F · DENV2_NGC_Fab_C10 28degree (1Fab:3E) · the same entry in another collection · chain B against B, 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 P14340
- Elsewhere: RCSB PDB 7V3F · PDBe 7V3F · UniProt P14340
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