Research workbench
Yeast 26S proteasome bound to ubiquitinated substrate (5D motor state)
Analyse Yeast 26S proteasome bound to ubiquitinated substrate (5D motor state) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EF1
- Type
- protein
- Length
- 3,294 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit alpha type-1; Proteasome subunit alpha type-2; Proteasome subunit…
- EC
- 3.4.25.1
- UniProt
- P21243, P23639, P23638, P40303, P32379, P40302, P21242, P33299, P40327, Q01939, P33298, P53549, P33297
- Ligands
- ATP, ADP
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 14 distinct chains · 36% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 239 | 37% helix, 17% strand | P21243 |
| B | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 250 | 34% helix, 19% strand | P23639 |
| C | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 238 | 33% helix, 19% strand | P23638 |
| D | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 234 | 34% helix, 17% strand | P40303 |
| E | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 242 | 33% helix, 18% strand | P32379 |
| F | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 233 | 33% helix, 22% strand | P40302 |
| G | Probable proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 243 | 35% helix, 21% strand | P21242 |
| H | 26S proteasome regulatory subunit 7 homolog | protein | 254 | 41% helix, 4% strand | P33299 |
| I | 26S proteasome regulatory subunit 4 homolog | protein | 271 | 36% helix, 3% strand | P40327 |
| J | 26S proteasome regulatory subunit 8 homolog | protein | 273 | 39% helix, 5% strand | Q01939 |
| K | 26S proteasome regulatory subunit 6B homolog | protein | 276 | 34% helix, 1% strand | P33298 |
| L | 26S proteasome subunit RPT4 | protein | 264 | 46% helix, 4% strand | P53549 |
| M | 26S proteasome regulatory subunit 6A | protein | 262 | 40% helix, 6% strand | P33297 |
| s | Model substrate polypeptide | protein | 15 | 0% helix, 0% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains H, I, J, K
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains 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 | 1128 | 0.90 | 0.92 | 178 | empty |
| 2 | 987 | 0.87 | 0.88 | 128 | empty |
| 3 | 965 | 0.85 | 0.87 | 115 | ATP |
| 4 | 1171 | 0.85 | 0.86 | 158 | ADP |
| 5 | 693 | 0.84 | 0.88 | 106 | empty |
Interfaces
36 interfaces between chains.
- J–K · 1542 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 1346 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1345 Ų buried · 8 hydrogen bonds · protein-protein
- A–G · 1344 Ų buried · 15 hydrogen bonds · protein-protein
- I–J · 1331 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6EF1 · Yeast 26S proteasome bound to ubiquitinated substrate (5D motor state) · the same entry in another collection · chain s against s, 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 P21243
- Every structure of UniProt P23639
- Every structure of UniProt P23638
- Every structure of UniProt P40303
- Every structure of UniProt P32379
- Every structure of UniProt P40302
- Every structure of UniProt P21242
- Every structure of UniProt P33299
- Every structure of UniProt P40327
- Every structure of UniProt Q01939
- Every structure of UniProt P33298
- Every structure of UniProt P53549
- Every structure of UniProt P33297
- Elsewhere: RCSB PDB 6EF1 · PDBe 6EF1 · UniProt P21243 · UniProt P23639 · UniProt P23638 · UniProt P40303 · UniProt P32379 · UniProt P40302 · UniProt P21242 · UniProt P33299 · UniProt P40327 · UniProt Q01939 · UniProt P33298 · UniProt P53549 · UniProt P33297
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