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Implications for interactions of proteasome with pan and PA700 from the 1.9 a structure of a proteasome-11S activator complex

Analyse Implications for interactions of proteasome with pan and PA700 from the 1.9 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YA7
Type: protein
Length: 4,536 residues
Chains: 21
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proteasome alpha subunit; Proteasome beta subunit; Proteasome activator protein PA26
EC: 3.4.25.1
UniProt: P25156, P28061
Ligands: SO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 48% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Proteasome alpha subunit (EC 3.4.25.1)	protein	227	33% helix, 26% strand	P25156
H, I, J, K, L, M, N	Proteasome beta subunit (EC 3.4.25.1)	protein	203	37% helix, 31% strand	P28061
O, P, Q, R, S, T, U	Proteasome activator protein PA26	protein	218	73% helix, 1% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 21 copies · chains A, B, H, C, I, D, J, E, K, F, L, G, M, N
GOL · Glycerol · additive · 7 copies · chains H, I, J, K, L, M, N

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

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	1073	0.82	0.83	111	SO4
2	743	0.81	0.85	92	SO4
3	993	0.81	0.82	113	SO4
4	919	0.81	0.83	99	SO4
5	1021	0.81	0.82	108	SO4

Interfaces

56 interfaces between chains.

P–Q · 2229 Å² buried · 36 hydrogen bonds · protein-protein
R–S · 2224 Å² buried · 41 hydrogen bonds · protein-protein
Q–R · 2191 Å² buried · 42 hydrogen bonds · protein-protein
S–T · 2174 Å² buried · 39 hydrogen bonds · protein-protein
O–P · 2163 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

1YA7 · Implications for interactions of proteasome with PAN and PA700 from the 1.9 A structure… · the same entry in another collection · chain T against T, 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 P25156
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Elsewhere: RCSB PDB 1YA7 · PDBe 1YA7 · UniProt P25156 · UniProt P28061

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