Research workbench

PIKFYVE/FIG4/VAC14 complex centered on VAC14 - MAP1

Analyse PIKFYVE/FIG4/VAC14 complex centered on VAC14 - MAP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7K1Y
Type: protein
Length: 2,612 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VAC14
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 4 distinct chains · 88% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, D	VAC14	protein	526	88% helix, 0% strand	—
C	VAC14	protein	499	87% helix, 0% strand	—
E	VAC14	protein	529	88% helix, 0% strand	—
G	VAC14	protein	532	88% helix, 0% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	988	0.79	0.81	121	empty
2	1161	0.76	0.79	134	empty
3	743	0.75	0.80	100	empty
4	702	0.75	0.80	99	empty
5	1026	0.74	0.77	119	empty

Interfaces

5 interfaces between chains.

B–G · 159 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 136 Å² buried · 0 hydrogen bonds · protein-protein
E–G · 100 Å² buried · 0 hydrogen bonds · protein-protein
D–E · 86 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 56 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7K1Y · PIKfyve/Fig4/Vac14 complex centered on Vac14 - map1 · the same entry in another collection · chain B against B, 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
Elsewhere: RCSB PDB 7K1Y · PDBe 7K1Y

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