Research workbench
Yeast 26S proteasome bound to ubiquitinated substrate (1D* motor state)
Analyse Yeast 26S proteasome bound to ubiquitinated substrate (1D* motor state) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EF0
- Type
- protein
- Length
- 3,318 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
- ADP, ATP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 14 distinct chains · 33% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 238 | 26% helix, 16% strand | P21243 |
| B | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 250 | 26% helix, 17% strand | P23639 |
| C | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 244 | 28% helix, 17% strand | P23638 |
| D | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 242 | 33% helix, 17% strand | P40303 |
| E | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 249 | 31% helix, 16% strand | P32379 |
| F | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 234 | 28% helix, 21% strand | P40302 |
| G | Probable proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 246 | 37% helix, 17% strand | P21242 |
| H | 26S proteasome regulatory subunit 7 homolog | protein | 257 | 37% helix, 5% strand | P33299 |
| I | 26S proteasome regulatory subunit 4 homolog | protein | 271 | 38% helix, 4% strand | P40327 |
| J | 26S proteasome regulatory subunit 8 homolog | protein | 272 | 35% helix, 4% strand | Q01939 |
| K | 26S proteasome regulatory subunit 6B homolog | protein | 272 | 35% helix, 2% strand | P33298 |
| L | 26S proteasome subunit RPT4 | protein | 273 | 37% helix, 4% strand | P53549 |
| M | 26S proteasome regulatory subunit 6A | protein | 258 | 35% helix, 3% strand | P33297 |
| s | Model substrate polypeptide | protein | 12 | 0% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains H, I, L, M
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains I, J, K, L
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 | 660 | 0.84 | 0.88 | 75 | empty |
| 2 | 685 | 0.83 | 0.87 | 86 | empty |
| 3 | 1057 | 0.82 | 0.83 | 111 | empty |
| 4 | 859 | 0.82 | 0.84 | 88 | ATP |
| 5 | 1110 | 0.81 | 0.82 | 127 | empty |
Interfaces
36 interfaces between chains.
- J–K · 1762 Ų buried · 7 hydrogen bonds · protein-protein
- K–L · 1697 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1523 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1347 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1347 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6EF0 · Yeast 26S proteasome bound to ubiquitinated substrate (1D* 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 6EF0 · PDBe 6EF0 · 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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