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Helical MYD88 death domain filament

Analyse Helical MYD88 death domain filament in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6I3N
Type: protein
Length: 1,339 residues
Chains: 13
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Myeloid differentiation primary response protein MYD88
UniProt: H0Y4G9
Pockets: 20 · best druggability 0.69

Structure

electron microscopy · 1 distinct chain · 64% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
M, I, J, K, H, L, B, F, C, D, A, E, G	Myeloid differentiation primary response protein MYD88	protein	103	64% helix, 0% strand	H0Y4G9

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	487	0.69	0.80	54	empty
2	298	0.67	0.83	62	empty
3	398	0.64	0.79	41	empty
4	262	0.63	0.81	47	empty
5	219	0.62	0.82	38	empty

Interfaces

31 interfaces between chains.

K–H · 673 Å² buried · 10 hydrogen bonds · protein-protein
J–G · 671 Å² buried · 10 hydrogen bonds · protein-protein
D–G · 667 Å² buried · 11 hydrogen bonds · protein-protein
F–C · 664 Å² buried · 11 hydrogen bonds · protein-protein
H–E · 664 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6I3N · Helical MyD88 death domain filament · the same entry in another collection · chain M against M, 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 H0Y4G9
Elsewhere: RCSB PDB 6I3N · PDBe 6I3N · UniProt H0Y4G9

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