MolNFT v1 · #151125 · protein
Pan-proteasome in state 2
6HE9 · Proteasome subunit alpha: “Pan-proteasome in state 2”. Electron microscopy, 3 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.86). MolNFT v1 #151125 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6HE9
- 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 0.86
Structure
electron microscopy · 4 distinct chains · 40% helix, 21% 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 | 42% helix, 24% strand | O29760 |
| a, b, c, d, e, f, g | Proteasome subunit alpha (EC 3.4.25.1) | protein | 237 | 39% helix, 24% 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 | 35% helix, 29% strand | Q9P996 |
| H, I, K, L, M, J | Proteasome-activating nucleotidase | protein | 390 | 43% helix, 13% strand | O28303 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains H, I, J, K, L
- ADP · Adenosine-5'-diphosphate · ligand · chains L, M
- 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.86 | 0.87 | 95 | ADP, MG |
| 2 | 312 | 0.83 | 0.93 | 42 | ATP, MG |
| 3 | 1100 | 0.81 | 0.83 | 104 | empty |
| 4 | 901 | 0.80 | 0.82 | 85 | empty |
| 5 | 485 | 0.79 | 0.86 | 50 | ATP, MG |
Interfaces
112 interfaces between chains.
- K–J · 5038 Ų buried · 35 hydrogen bonds · protein-protein
- H–I · 5017 Ų buried · 34 hydrogen bonds · protein-protein
- L–M · 4382 Ų buried · 32 hydrogen bonds · protein-protein
- I–J · 2977 Ų buried · 26 hydrogen bonds · protein-protein
- K–L · 2844 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6HE9 · PAN-proteasome in state 2 · the same entry in another collection · chain C against C, 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 6HE9 · PDBe 6HE9 · UniProt O29760 · UniProt Q9P996 · UniProt O28303
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