Research workbench
Influenza a M2 proton channel wild type tm domain bound to R- rimantadine
Analyse Influenza a M2 proton channel wild type tm domain bound to R- rimantadine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6US9
- Type
- protein
- Length
- 376 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix protein 2
- UniProt
- D5F6K1
- Ligands
- RIM, NH2, CL
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 89% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, G, H, I, L, N | Matrix protein 2 | protein | 24 | 88% helix, 0% strand | D5F6K1 |
| C, D, F, J, K, M, O, P | Matrix protein 2 | protein | 23 | 91% helix, 0% strand | D5F6K1 |
Ligands and binding sites
- RIM · Rimantadine · ligand · 4 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- NH2 · Amino group · ion · 16 copies · chains A, B, L, C, D, N, E, F, G, H, I, J, K, M, O, P
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.82 | 0.97 | 30 | RIM |
| 2 | 173 | 0.82 | 0.97 | 29 | RIM |
| 3 | 180 | 0.82 | 0.97 | 30 | RIM |
| 4 | 170 | 0.81 | 0.97 | 29 | RIM |
| 5 | 1110 | 0.77 | 0.79 | 63 | CL |
Interfaces
40 interfaces between chains.
- I–L · 498 Ų buried · 3 hydrogen bonds · protein-protein
- K–L · 496 Ų buried · 2 hydrogen bonds · protein-protein
- E–H · 494 Ų buried · 1 hydrogen bond · protein-protein
- G–H · 493 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 492 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6US9 · Influenza A M2 proton channel wild type TM domain bound to R-rimantadine · 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 D5F6K1
- Elsewhere: RCSB PDB 6US9 · PDBe 6US9 · UniProt D5F6K1
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