Research workbench
Binding of the C-terminal gqyl motif of the bacterial proteasome activator bpa to the 20S proteasome
Analyse Binding of the C-terminal gqyl motif of the bacterial proteasome activator bpa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LZP
- Type
- protein
- Length
- 6,182 residues
- Chains
- 35
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit alpha; Bacterial proteasome activator; Proteasome subunit beta
- EC
- 3.4.25.1
- UniProt
- P9WHU1, P9WKX3, P9WHT9
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 7 distinct chains · 42% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0, 2, 4, 6, 8, H, J, S, W, Y | Proteasome subunit alpha (EC 3.4.25.1) | protein | 215 | 42% helix, 26% strand | P9WHU1 |
| 1, 3, 5, 7, V, X, Z | Bacterial proteasome activator | protein | 5 | 0% helix, 20% strand | P9WKX3 |
| A, E, F, G, K, L | Proteasome subunit beta (EC 3.4.25.1) | protein | 222 | 41% helix, 29% strand | P9WHT9 |
| B, M, Q | Proteasome subunit alpha (EC 3.4.25.1) | protein | 214 | 43% helix, 26% strand | P9WHU1 |
| C, I, O, R, T, U | Proteasome subunit beta (EC 3.4.25.1) | protein | 223 | 41% helix, 30% strand | P9WHT9 |
| D | Proteasome subunit alpha (EC 3.4.25.1) | protein | 217 | 42% helix, 25% strand | P9WHU1 |
| N, P | Proteasome subunit beta (EC 3.4.25.1) | protein | 234 | 41% helix, 29% strand | P9WHT9 |
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 | 1181 | 0.86 | 0.87 | 114 | empty |
| 2 | 611 | 0.84 | 0.89 | 47 | empty |
| 3 | 584 | 0.84 | 0.89 | 50 | empty |
| 4 | 607 | 0.84 | 0.89 | 50 | empty |
| 5 | 579 | 0.84 | 0.89 | 45 | empty |
Interfaces
84 interfaces between chains.
- G–N · 804 Ų buried · 14 hydrogen bonds · protein-protein
- E–P · 789 Ų buried · 14 hydrogen bonds · protein-protein
- K–L · 755 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 755 Ų buried · 14 hydrogen bonds · protein-protein
- F–I · 754 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5LZP · Binding of the C-terminal GQYL motif of the bacterial proteasome activator Bpa to the 20S… · the same entry in another collection · chain A against A, 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 P9WHU1
- Every structure of UniProt P9WKX3
- Every structure of UniProt P9WHT9
- Elsewhere: RCSB PDB 5LZP · PDBe 5LZP · UniProt P9WHU1 · UniProt P9WKX3 · UniProt P9WHT9
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