Research workbench
Pan-proteasome in state 3
Analyse Pan-proteasome in state 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HEA
- 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 · 41% helix, 20% 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 | 41% helix, 24% strand | O29760 |
| a, b, c, d, e, f, g | Proteasome subunit alpha (EC 3.4.25.1) | protein | 237 | 38% helix, 23% 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, 28% strand | Q9P996 |
| H, I, K, L, M, J | Proteasome-activating nucleotidase | protein | 390 | 45% helix, 13% strand | O28303 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains H, I, J, M, K
- ADP · Adenosine-5'-diphosphate · ligand · chains K, L
- MG · Magnesium ion · metal · 5 copies · chains H, I, K, L, M, J
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 | 833 | 0.82 | 0.84 | 95 | ATP, MG |
| 2 | 495 | 0.81 | 0.88 | 60 | ATP, MG |
| 3 | 976 | 0.79 | 0.81 | 117 | empty |
| 4 | 1019 | 0.79 | 0.81 | 87 | empty |
| 5 | 580 | 0.79 | 0.85 | 65 | ATP, MG |
Interfaces
110 interfaces between chains.
- H–I · 4913 Ų buried · 36 hydrogen bonds · protein-protein
- K–J · 4770 Ų buried · 34 hydrogen bonds · protein-protein
- L–M · 3855 Ų buried · 27 hydrogen bonds · protein-protein
- I–J · 3193 Ų buried · 37 hydrogen bonds · protein-protein
- H–M · 2740 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6HEA · PAN-proteasome in state 3 · 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 O29760
- Every structure of UniProt Q9P996
- Every structure of UniProt O28303
- Elsewhere: RCSB PDB 6HEA · PDBe 6HEA · UniProt O29760 · UniProt Q9P996 · UniProt O28303
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