Research workbench
26S proteasome, s1 state
Analyse 26S proteasome, s1 state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FVT
- Type
- protein
- Length
- 14,028 residues
- Chains
- 47
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.1
- Source
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Molecule
- Proteasome subunit alpha type-1; Proteasome subunit alpha type-2; Proteasome subunit…
- EC
- 3.4.25.1, 3.4.19.12
- UniProt
- P21243, P23639, P23638, P40303, P32379, P40302, P21242, P38624, P25043, P25451, P22141, P30656, P23724, P30657, P38886, P43588, P32496, O13563, O94742, P38764, P32565, P40016, Q12250, Q12377, Q06103, Q08723, Q04062, P33299, P40327, P33298, P53549, P33297, Q01939
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 4.1 · 35 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a, A | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 241 | 34% helix, 21% strand | P21243 |
| b, B | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 249 | 33% helix, 25% strand | P23639 |
| c, C | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 244 | 37% helix, 24% strand | P23638 |
| d | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 251 | 39% helix, 22% strand | P40303 |
| e, E | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 244 | 33% helix, 25% strand | P32379 |
| f, F | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 231 | 29% helix, 21% strand | P40302 |
| g, G | Probable proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 245 | 36% helix, 26% strand | P21242 |
| h, 1 | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 196 | 33% helix, 33% strand | P38624 |
| i, 2 | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 226 | 28% helix, 35% strand | P25043 |
| j, 3 | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 29% helix, 31% strand | P25451 |
| k, 4 | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 195 | 33% helix, 33% strand | P22141 |
| l, 5 | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 212 | 35% helix, 32% strand | P30656 |
| m, 6 | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 222 | 29% helix, 32% strand | P23724 |
| n | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 232 | 27% helix, 30% strand | P30657 |
| D | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 237 | 35% helix, 24% strand | P40303 |
| 7 | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 229 | 31% helix, 30% strand | P30657 |
| W | 26S proteasome regulatory subunit RPN10 | protein | 197 | 35% helix, 19% strand | P38886 |
| V | Ubiquitin carboxyl-terminal hydrolase RPN11 (EC 3.4.19.12) | protein | 289 | 46% helix, 15% strand | P43588 |
| T | 26S proteasome regulatory subunit RPN12 | protein | 266 | 72% helix, 1% strand | P32496 |
| X | 26S proteasome regulatory subunit RPN13 | protein | 127 | 9% helix, 27% strand | O13563 |
| Y | 26S proteasome complex subunit SEM1 | protein | 89 | 37% helix, 0% strand | O94742 |
| Z | 26S proteasome regulatory subunit RPN1 | protein | 906 | 60% helix, 2% strand | P38764 |
| N | 26S proteasome regulatory subunit RPN2 | protein | 922 | 60% helix, 2% strand | P32565 |
| S | 26S proteasome regulatory subunit RPN3 | protein | 475 | 68% helix, 2% strand | P40016 |
| P | 26S proteasome regulatory subunit RPN5 | protein | 440 | 72% helix, 2% strand | Q12250 |
| Q | 26S proteasome regulatory subunit RPN6 | protein | 434 | 71% helix, 2% strand | Q12377 |
| R | 26S proteasome regulatory subunit RPN7 | protein | 405 | 70% helix, 3% strand | Q06103 |
| U | 26S proteasome regulatory subunit RPN8 | protein | 304 | 50% helix, 19% strand | Q08723 |
| O | 26S proteasome regulatory subunit RPN9 | protein | 388 | 72% helix, 4% strand | Q04062 |
| H | 26S proteasome regulatory subunit 7 homolog | protein | 426 | 37% helix, 15% strand | P33299 |
| I | 26S proteasome regulatory subunit 4 homolog | protein | 385 | 43% helix, 14% strand | P40327 |
| K | 26S proteasome regulatory subunit 6B homolog | protein | 394 | 38% helix, 13% strand | P33298 |
| L | 26S proteasome subunit RPT4 | protein | 388 | 43% helix, 16% strand | P53549 |
| M | 26S proteasome regulatory subunit 6A | protein | 421 | 39% helix, 12% strand | P33297 |
| J | 26S proteasome regulatory subunit 8 homolog | protein | 405 | 46% helix, 16% strand | Q01939 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains H, I, J, K, L, M
- ADP · Adenosine-5'-diphosphate · ligand · chains J
- MG · Magnesium ion · metal · 6 copies · chains H, M, 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 | 1112 | 0.84 | 0.85 | 117 | empty |
| 2 | 783 | 0.83 | 0.86 | 80 | empty |
| 3 | 634 | 0.83 | 0.88 | 71 | ATP, MG |
| 4 | 912 | 0.82 | 0.84 | 115 | ATP, MG |
| 5 | 1163 | 0.82 | 0.83 | 109 | ADP, MG |
Interfaces
175 interfaces between chains.
- L–M · 5484 Ų buried · 50 hydrogen bonds · protein-protein
- H–I · 4577 Ų buried · 40 hydrogen bonds · protein-protein
- V–U · 4112 Ų buried · 25 hydrogen bonds · protein-protein
- H–M · 3541 Ų buried · 29 hydrogen bonds · protein-protein
- K–J · 3525 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- P53549 · AlphaFold monomer V2.0 prediction for 26S proteasome subunit RPT4 (P53549) · a predicted model of the same protein · chain L against A, TM-score 0.95
- P33298 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit 6B homolog… · a predicted model of the same protein · chain K against A, TM-score 0.93
- Q06103 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit RPN7 (Q06103) · a predicted model of the same protein · chain R against A, TM-score 0.93
- P38886 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit RPN10 (P38886) · a predicted model of the same protein · chain W against A, TM-score 0.93
- Q08723 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit RPN8 (Q08723) · a predicted model of the same protein · chain U against A, TM-score 0.92
- P40016 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit RPN3 (P40016) · a predicted model of the same protein · chain S against A, TM-score 0.92
- P33299 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit 7 homolog (P33299) · a predicted model of the same protein · chain H against A, TM-score 0.91
- Q12250 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit RPN5 (Q12250) · a predicted model of the same protein · chain P against A, TM-score 0.90
- P43588 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase RPN11 (P43588) · a predicted model of the same protein · chain V against A, TM-score 0.90
- P33297 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit 6A (P33297) · a predicted model of the same protein · chain M against A, TM-score 0.90
- Q04062 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit RPN9 (Q04062) · a predicted model of the same protein · chain O against A, TM-score 0.89
- P40327 · AlphaFold monomer V2.0 prediction for 26S proteasome regulatory subunit 4 homolog (P40327) · a predicted model of the same protein · chain I against A, TM-score 0.88
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 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 P38886
- Every structure of UniProt P43588
- Every structure of UniProt P32496
- Every structure of UniProt O13563
- Every structure of UniProt O94742
- Every structure of UniProt P38764
- Every structure of UniProt P32565
- Every structure of UniProt P40016
- Every structure of UniProt Q12250
- Every structure of UniProt Q12377
- Every structure of UniProt Q06103
- Every structure of UniProt Q08723
- Every structure of UniProt Q04062
- Every structure of UniProt P33299
- Every structure of UniProt P40327
- Every structure of UniProt P33298
- Every structure of UniProt P53549
- Every structure of UniProt P33297
- Every structure of UniProt Q01939
- Elsewhere: RCSB PDB 6FVT · PDBe 6FVT · UniProt P21243 · UniProt P23639 · UniProt P23638 · UniProt P40303 · UniProt P32379 · UniProt P40302 · UniProt P21242 · UniProt P38624 · UniProt P25043 · UniProt P25451 · UniProt P22141 · UniProt P30656 · UniProt P23724 · UniProt P30657 · UniProt P38886 · UniProt P43588 · UniProt P32496 · UniProt O13563 · UniProt O94742 · UniProt P38764 · UniProt P32565 · UniProt P40016 · UniProt Q12250 · UniProt Q12377 · UniProt Q06103 · UniProt Q08723 · UniProt Q04062 · UniProt P33299 · UniProt P40327 · UniProt P33298 · UniProt P53549 · UniProt P33297 · UniProt Q01939
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