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Influenza a M2 proton channel wild type tm domain bound to S- rimantadine

Analyse Influenza a M2 proton channel wild type tm domain bound to S- rimantadine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6US8
Type: protein
Length: 380 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Matrix protein 2
UniProt: D5F6K1
Ligands: EU7, NH2, CL
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 88% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, N, O, P	Matrix protein 2	protein	23	91% helix, 0% strand	D5F6K1
B, D, I, J, L, M	Matrix protein 2	protein	24	88% helix, 0% strand	D5F6K1
F, H, K	Matrix protein 2	protein	25	84% helix, 0% strand	D5F6K1

Ligands and binding sites

EU7 · (1S)-1-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]decan-1-yl]ethan-1-amine · ligand · 12 copies · chains A, B, C, D, F, G, E, H, I, J, K, L, M, N, O, P
NH2 · Amino group · ion · 16 copies · chains A, F, B, C, D, E, N, G, H, I, J, K, L, 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

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	177	0.82	0.97	29	EU7
2	177	0.81	0.96	30	EU7
3	175	0.81	0.96	29	EU7
4	171	0.81	0.97	30	EU7
5	838	0.71	0.75	46	EU7

Interfaces

38 interfaces between chains.

J–K · 506 Å² buried · 3 hydrogen bonds · protein-protein
G–H · 500 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 498 Å² buried · 4 hydrogen bonds · protein-protein
M–P · 493 Å² buried · 4 hydrogen bonds · protein-protein
K–L · 492 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6US8 · Influenza A M2 proton channel wild type TM domain bound to S-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 6US8 · PDBe 6US8 · UniProt D5F6K1

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