Research workbench
Influenza a M2 transmembrane domain bound to rimantadine
Analyse Influenza a M2 transmembrane domain bound to rimantadine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BKL
- Type
- protein
- Length
- 186 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix protein 2
- UniProt
- Q20MD5
- Ligands
- EU7, RIM
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 89% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Matrix protein 2 | protein | 24 | 88% helix, 0% strand | Q20MD5 |
| B, C, D, F, G, H | Matrix protein 2 | protein | 23 | 91% helix, 0% strand | Q20MD5 |
Ligands and binding sites
- EU7 · (1S)-1-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]decan-1-yl]ethan-1-amine · ligand · 2 copies · chains A, B, C, D, E, F, G, H
- RIM · Rimantadine · ligand · 2 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.82 | 0.97 | 30 | EU7, RIM |
| 2 | 170 | 0.81 | 0.97 | 29 | RIM, EU7 |
Interfaces
17 interfaces between chains.
- E–H · 508 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 495 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 490 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 485 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 478 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6BKL · Influenza A M2 transmembrane domain bound to 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 Q20MD5
- Elsewhere: RCSB PDB 6BKL · PDBe 6BKL · UniProt Q20MD5
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