MolNFT v1 · #144143 · protein
Influenza a M2 transmembrane domain bound to amantadine
6BKK · Matrix protein 2: “Influenza a M2 transmembrane domain bound to amantadine”. X-ray diffraction, 3 ligands (ACE, 308, CL), 3 pockets (best druggability 0.83). MolNFT v1 #144143 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6BKK
- Type
- protein
- Length
- 200 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix protein 2
- UniProt
- Q20MD5
- Ligands
- ACE, 308, CL
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 84% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Matrix protein 2 | protein | 25 | 84% helix, 0% strand | Q20MD5 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 5 copies · chains A, B, C, E, F, G, H
- 308 · (3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine · ligand · 2 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.83 | 0.98 | 29 | 308 |
| 2 | 171 | 0.83 | 0.98 | 29 | 308 |
| 3 | 78 | 0.32 | 0.73 | 16 | empty |
Interfaces
17 interfaces between chains.
- C–D · 596 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 578 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 574 Ų buried · 4 hydrogen bonds · protein-protein
- E–H · 573 Ų buried · 2 hydrogen bonds · protein-protein
- F–G · 570 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 6BKK · Influenza A M2 transmembrane domain bound to amantadine · 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 6BKK · PDBe 6BKK · UniProt Q20MD5
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