Research workbench
DENV2_NGC_FAB_C10 28DEGREES (3FAB:3E)
Analyse DENV2_NGC_FAB_C10 28DEGREES (3FAB:3E) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V3H
- Type
- protein
- Length
- 2,409 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein E; Small envelope protein M; C10 IgG light chain variable region; C10…
- UniProt
- P14340
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 15% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Envelope protein E | protein | 495 | 16% helix, 32% strand | P14340 |
| E, D, F | Small envelope protein M | protein | 72 | 53% helix, 1% strand | P14340 |
| I, G, K | C10 IgG light chain variable region | protein | 127 | 2% helix, 36% strand | — |
| M, H, L | C10 IgG heavy chain variable region | protein | 109 | 0% helix, 39% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, K, A, G, C, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.84 | 0.86 | 93 | empty |
| 2 | 904 | 0.79 | 0.82 | 96 | empty |
| 3 | 1192 | 0.79 | 0.81 | 113 | empty |
| 4 | 971 | 0.78 | 0.80 | 108 | empty |
| 5 | 88 | 0.74 | 0.97 | 28 | empty |
Interfaces
24 interfaces between chains.
- C–F · 1755 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 1713 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1713 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1638 Ų buried · 15 hydrogen bonds · protein-protein
- B–A · 1284 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 7V3H · DENV2_NGC_Fab_C10 28degrees (3Fab: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 7V3H · PDBe 7V3H · UniProt P14340
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