Research workbench
Structure of archeabacterial 20S proteasome- PA26 complex
Analyse Structure of archeabacterial 20S proteasome- PA26 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YAU
- Type
- protein
- Length
- 4,501 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 | 222 | 34% helix, 27% 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 · 25 copies · chains A, G, N, B, H, C, I, D, J, E, K, F, L, M
- 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.82 | 0.84 | 93 | SO4 |
| 2 | 1033 | 0.81 | 0.82 | 97 | SO4 |
| 3 | 974 | 0.80 | 0.82 | 101 | SO4 |
| 4 | 1085 | 0.80 | 0.81 | 110 | SO4 |
| 5 | 418 | 0.79 | 0.88 | 57 | SO4 |
Interfaces
56 interfaces between chains.
- Q–R · 2224 Ų buried · 38 hydrogen bonds · protein-protein
- R–S · 2198 Ų buried · 39 hydrogen bonds · protein-protein
- O–U · 2193 Ų buried · 39 hydrogen bonds · protein-protein
- T–U · 2173 Ų buried · 32 hydrogen bonds · protein-protein
- P–Q · 2172 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 1YAU · Structure of Archeabacterial 20S proteasome- PA26 complex · the same entry in another collection · chain U against U, 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
- Every structure of UniProt P28061
- Elsewhere: RCSB PDB 1YAU · PDBe 1YAU · UniProt P25156 · UniProt P28061
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