Research workbench
2.8 a resolution reconstruction of the thermoplasma acidophilum 20S proteasome using cryo-electron microscopy
Analyse 2.8 a resolution reconstruction of the thermoplasma acidophilum 20S proteasome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BDF
- Type
- protein
- Length
- 5,908 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit alpha; Proteasome subunit beta
- EC
- 3.4.25.1
- UniProt
- P25156, P28061
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 2 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, W, Y, 0 | Proteasome subunit alpha (EC 3.4.25.1) | protein | 221 | 36% helix, 27% strand | P25156 |
| B, D, F, H, J, L, N, P, R, T, V, X, Z, 1 | Proteasome subunit beta (EC 3.4.25.1) | protein | 201 | 35% helix, 30% strand | P28061 |
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 | 986 | 0.76 | 0.78 | 103 | empty |
| 2 | 754 | 0.76 | 0.80 | 71 | empty |
| 3 | 721 | 0.75 | 0.81 | 69 | empty |
| 4 | 752 | 0.75 | 0.80 | 71 | empty |
| 5 | 731 | 0.75 | 0.80 | 70 | empty |
Interfaces
70 interfaces between chains.
- O–Q · 1274 Ų buried · 24 hydrogen bonds · protein-protein
- Q–S · 1274 Ų buried · 24 hydrogen bonds · protein-protein
- Y–0 · 1273 Ų buried · 24 hydrogen bonds · protein-protein
- S–U · 1270 Ų buried · 24 hydrogen bonds · protein-protein
- E–G · 1270 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6BDF · 2.8 A resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using… · the same entry in another collection · chain K against K, 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 6BDF · PDBe 6BDF · UniProt P25156 · UniProt P28061
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