Research workbench
Nanobody targeting influenza a matrix protein 2 ectodomain (M2E)
Analyse Nanobody targeting influenza a matrix protein 2 ectodomain (M2E) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S0Y
- Type
- protein
- Length
- 266 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M2E-vhh-23M; Matrix protein 2
- UniProt
- B2VLW8
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M2E-vhh-23M | protein | 120 | 5% helix, 56% strand | — |
| B | M2E-vhh-23M | protein | 119 | 5% helix, 52% strand | — |
| C | Matrix protein 2 | protein | 14 | 0% helix, 36% strand | B2VLW8 |
| D | Matrix protein 2 | protein | 13 | 0% helix, 23% strand | B2VLW8 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.55 | 0.83 | 24 | empty |
| 2 | 50 | 0.41 | 0.82 | 15 | empty |
| 3 | 53 | 0.40 | 0.82 | 16 | empty |
| 4 | 66 | 0.40 | 0.80 | 15 | empty |
| 5 | 95 | 0.37 | 0.75 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–C · 668 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 593 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 325 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 68 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6S0Y · Nanobody targeting influenza A matrix protein 2 ectodomain (M2e) · 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 B2VLW8
- Elsewhere: RCSB PDB 6S0Y · PDBe 6S0Y · UniProt B2VLW8
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