MolNFT v1 · #147504 · protein
Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state)
6EF3 · Proteasome subunit beta type-1: “Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state)”. Electron microscopy, 2 ligands (ATP, ADP), 20 pockets (best druggability 0.83). MolNFT v1 #147504 on GenesisL1: 3D structure…
- PDB
- 6EF3
- Type
- protein
- Length
- 5,824 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit beta type-1; Proteasome subunit beta type-2; Proteasome subunit beta…
- EC
- 3.4.25.1, 3.4.19.12
- UniProt
- P38624, P25043, P25451, P22141, P30656, P23724, P30657, P21243, P23639, P23638, P40303, P32379, P40302, P21242, P33299, P40327, Q01939, P33298, P53549, P33297, P43588, P0CH08
- Ligands
- ATP, ADP
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 24 distinct chains · 32% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 196 | 30% helix, 27% strand | P38624 |
| 2 | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 224 | 26% helix, 24% strand | P25043 |
| 3 | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 28% helix, 26% strand | P25451 |
| 4 | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 195 | 24% helix, 24% strand | P22141 |
| 5 | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 212 | 32% helix, 31% strand | P30656 |
| 6 | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 220 | 22% helix, 25% strand | P23724 |
| 7 | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 208 | 30% helix, 24% strand | P30657 |
| A | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 247 | 31% helix, 18% 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 | 242 | 29% helix, 14% strand | P23638 |
| D | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 241 | 30% helix, 17% strand | P40303 |
| E | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 249 | 24% helix, 16% strand | P32379 |
| F | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 234 | 32% helix, 17% strand | P40302 |
| G | Probable proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 246 | 34% helix, 21% strand | P21242 |
| H | 26S proteasome regulatory subunit 7 homolog | protein | 380 | 36% helix, 9% strand | P33299 |
| I | 26S proteasome regulatory subunit 4 homolog | protein | 384 | 36% helix, 9% strand | P40327 |
| J | 26S proteasome regulatory subunit 8 homolog | protein | 383 | 39% helix, 13% strand | Q01939 |
| K | 26S proteasome regulatory subunit 6B homolog | protein | 370 | 37% helix, 12% strand | P33298 |
| L | 26S proteasome subunit RPT4 | protein | 360 | 39% helix, 12% strand | P53549 |
| M | 26S proteasome regulatory subunit 6A | protein | 371 | 40% helix, 8% strand | P33297 |
| n | Proteasome subunit beta type-7 | protein | 15 | 0% helix, 0% strand | — |
| r | Ubiquitin carboxyl-terminal hydrolase RPN11 (EC 3.4.19.12) | protein | 280 | 38% helix, 13% strand | P43588 |
| s | Model substrate polypeptide | protein | 38 | 0% helix, 3% strand | — |
| u | Ubiquitin-60S ribosomal protein L40 | protein | 75 | 23% helix, 27% strand | P0CH08 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains H, I, J, K, M
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains 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 | 893 | 0.83 | 0.85 | 110 | ATP |
| 2 | 688 | 0.82 | 0.86 | 93 | empty |
| 3 | 635 | 0.81 | 0.85 | 88 | empty |
| 4 | 715 | 0.80 | 0.84 | 84 | empty |
| 5 | 1111 | 0.80 | 0.81 | 97 | empty |
Interfaces
74 interfaces between chains.
- H–I · 3742 Ų buried · 22 hydrogen bonds · protein-protein
- J–K · 3071 Ų buried · 20 hydrogen bonds · protein-protein
- H–M · 2516 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 2358 Ų buried · 12 hydrogen bonds · protein-protein
- L–M · 2047 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 6EF3 · Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state) · the same entry in another collection · chain C against C, 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 P38624
- Every structure of UniProt P25043
- Every structure of UniProt P25451
- Every structure of UniProt P22141
- Every structure of UniProt P30656
- Every structure of UniProt P23724
- Every structure of UniProt P30657
- 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
- Every structure of UniProt P43588
- Every structure of UniProt P0CH08
- Elsewhere: RCSB PDB 6EF3 · PDBe 6EF3 · UniProt P38624 · UniProt P25043 · UniProt P25451 · UniProt P22141 · UniProt P30656 · UniProt P23724 · UniProt P30657 · 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 · UniProt P43588 · UniProt P0CH08
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