MolNFT v1 · #151129 · protein

Pan-proteasome in state 5

6HED · Proteasome subunit alpha: “Pan-proteasome in state 5”. Electron microscopy, 3 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.82). MolNFT v1 #151129 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6HED
Type: protein
Length: 8,521 residues
Chains: 34
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proteasome subunit alpha; Proteasome subunit beta; Proteasome-activating nucleotidase
EC: 3.4.25.1
UniProt: O29760, Q9P996, O28303
Ligands: ATP, ADP, MG
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 4 distinct chains · 39% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Proteasome subunit alpha (EC 3.4.25.1)	protein	242	39% helix, 25% strand	O29760
a, b, c, d, e, f, g	Proteasome subunit alpha (EC 3.4.25.1)	protein	237	38% helix, 26% strand	O29760
1, h, 2, i, 3, j, 4, k, 5, l, 6, m, 7, n	Proteasome subunit beta (EC 3.4.25.1)	protein	202	36% helix, 29% strand	Q9P996
H, I, K, L, M, J	Proteasome-activating nucleotidase	protein	390	42% helix, 14% strand	O28303

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains H, I, K, L, M
ADP · Adenosine-5'-diphosphate · ligand · chains I, J
MG · Magnesium ion · metal · 5 copies · chains H, I, J, K, L, M

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	1140	0.82	0.83	123	ATP, MG
2	411	0.81	0.89	41	ATP, MG
3	505	0.78	0.86	47	ATP, MG
4	926	0.78	0.80	80	ADP, MG
5	1167	0.77	0.79	105	empty

Interfaces

106 interfaces between chains.

H–I · 4903 Å² buried · 31 hydrogen bonds · protein-protein
L–M · 4837 Å² buried · 52 hydrogen bonds · protein-protein
K–J · 3786 Å² buried · 31 hydrogen bonds · protein-protein
H–M · 3072 Å² buried · 40 hydrogen bonds · protein-protein
K–L · 2860 Å² buried · 27 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

6HED · PAN-proteasome in state 5 · the same entry in another collection · chain j against j, 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 O29760
Every structure of UniProt Q9P996
Every structure of UniProt O28303
Elsewhere: RCSB PDB 6HED · PDBe 6HED · UniProt O29760 · UniProt Q9P996 · UniProt O28303

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