MolNFT v1 · #155936 · protein
Cryo-EM structure of immature zika virus in complex with human antibody DV62.5 Fab
6LNT · Envelope protein: “Cryo-EM structure of immature zika virus in complex with human antibody DV62.5 Fab”. Electron microscopy, 7 pockets (best druggability 0.45). MolNFT v1 #155936 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6LNT
- Type
- protein
- Length
- 2,642 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein; Pre-membrane protein; Fab DV62.5 heavy-chain variable region; Fab…
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48
- UniProt
- A0A024B7W1
- Pockets
- 7 · best druggability 0.45
Structure
electron microscopy · 5 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Envelope protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 503 | 0% helix, 0% strand | A0A024B7W1 |
| D, E, F | Pre-membrane protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 163 | 0% helix, 0% strand | A0A024B7W1 |
| H, P | Fab DV62.5 heavy-chain variable region | protein | 120 | 0% helix, 0% strand | — |
| L, Q | Fab DV62.5 light-chain variable region | protein | 106 | 0% helix, 0% strand | — |
| M, N | Capsid protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 96 | 0% helix, 0% strand | A0A024B7W1 |
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.45 | 0.73 | 37 | empty |
| 2 | 96 | 0.36 | 0.72 | 31 | empty |
| 3 | 94 | 0.36 | 0.72 | 30 | empty |
| 4 | 72 | 0.33 | 0.73 | 29 | empty |
| 5 | 69 | 0.32 | 0.73 | 20 | empty |
Interfaces
9 interfaces between chains.
- B–E · 550 Ų buried · 0 hydrogen bonds · protein-protein
- M–N · 402 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 376 Ų buried · 0 hydrogen bonds · protein-protein
- C–F · 374 Ų buried · 0 hydrogen bonds · protein-protein
- A–H · 58 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6LNT · Cryo-EM structure of immature Zika virus in complex with human antibody DV62.5 Fab · 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 A0A024B7W1
- Elsewhere: RCSB PDB 6LNT · PDBe 6LNT · UniProt A0A024B7W1
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