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Cryo-EM structure of dengue virus serotype 2 strain PVP94-07 complexed with human antibody 2D22 Fab at 37 degrees C
Analyse Cryo-EM structure of dengue virus serotype 2 strain PVP94-07 complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A1Z
- Type
- protein
- Length
- 2,394 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein; Membrane glycoprotein; Antigen-binding fragment of human antibody 2D22…
- UniProt
- G9FRP5, V5TI05
- Pockets
- 5 · best druggability 0.43
Structure
electron microscopy · 4 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Envelope protein | protein | 495 | 0% helix, 0% strand | G9FRP5 |
| B, D, F | Membrane glycoprotein | protein | 72 | 0% helix, 0% strand | V5TI05 |
| G, I, K | Antigen-binding fragment of human antibody 2D22 - heavy chain | protein | 120 | 0% helix, 0% strand | — |
| H, J, L | Antigen-binding fragment of human antibody 2D22 - light chain | protein | 111 | 0% helix, 0% strand | — |
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.43 | 0.73 | 35 | empty |
| 2 | 88 | 0.35 | 0.73 | 28 | empty |
| 3 | 66 | 0.32 | 0.73 | 20 | empty |
| 4 | 76 | 0.32 | 0.72 | 22 | empty |
| 5 | 51 | 0.27 | 0.72 | 20 | empty |
Interfaces
19 interfaces between chains.
- E–F · 267 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 255 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 248 Ų buried · 0 hydrogen bonds · protein-protein
- C–E · 235 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 194 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5A1Z · Cryo-EM structure of Dengue virus serotype 2 strain PVP94-07 complexed with human… · 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 G9FRP5
- Every structure of UniProt V5TI05
- Elsewhere: RCSB PDB 5A1Z · PDBe 5A1Z · UniProt G9FRP5 · UniProt V5TI05
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