MolNFT v1 · #185976 · protein
Structure of the 26S proteasome-UBP6 complex in the si state (core particle and lid)
7QO3 · Proteasome subunit alpha type-1: “Structure of the 26S proteasome-UBP6 complex in the si state (core particle and lid)”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #185976 on GenesisL1: 3D structure, binding…
- PDB
- 7QO3
- Type
- protein
- Length
- 11,480 residues
- Chains
- 41
- 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, 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
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 27 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a, A | Proteasome subunit alpha type-1 | protein | 241 | 37% helix, 22% strand | P21243 |
| b, B | Proteasome subunit alpha type-2 | protein | 249 | 31% helix, 25% strand | P23639 |
| c, C | Proteasome subunit alpha type-3 | protein | 244 | 37% helix, 25% strand | P23638 |
| d, D | Proteasome subunit alpha type-4 | protein | 236 | 36% helix, 23% strand | P40303 |
| e, E | Proteasome subunit alpha type-5 | protein | 244 | 32% helix, 25% strand | P32379 |
| f, F | Proteasome subunit alpha type-6 | protein | 231 | 35% helix, 23% strand | P40302 |
| g, G | Probable proteasome subunit alpha type-7 | protein | 242 | 37% helix, 26% strand | P21242 |
| h, 1 | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 196 | 35% helix, 30% strand | P38624 |
| i, 2 | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 226 | 29% helix, 32% strand | P25043 |
| j, 3 | Proteasome subunit beta type-3 | protein | 204 | 33% helix, 35% strand | P25451 |
| k, 4 | Proteasome subunit beta type-4 | protein | 195 | 34% helix, 34% strand | P22141 |
| l, 5 | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 212 | 36% helix, 34% strand | P30656 |
| m, 6 | Proteasome subunit beta type-6 | protein | 222 | 29% helix, 30% strand | P23724 |
| n, 7 | Proteasome subunit beta type-7 | protein | 229 | 31% helix, 31% strand | P30657 |
| W | 26S proteasome regulatory subunit RPN10 | protein | 197 | 36% helix, 18% strand | P38886 |
| V | Ubiquitin carboxyl-terminal hydrolase RPN11 (EC 3.4.19.12) | protein | 289 | 43% helix, 19% strand | P43588 |
| T | 26S proteasome regulatory subunit RPN12 | protein | 266 | 71% helix, 2% strand | P32496 |
| X | 26S proteasome regulatory subunit RPN13 | protein | 127 | 9% helix, 29% strand | O13563 |
| Y | 26S proteasome complex subunit SEM1 | protein | 89 | 51% helix, 0% strand | O94742 |
| Z | 26S proteasome regulatory subunit RPN1 | protein | 906 | 60% helix, 2% strand | P38764 |
| N | 26S proteasome regulatory subunit RPN2 | protein | 832 | 64% helix, 3% strand | P32565 |
| S | 26S proteasome regulatory subunit RPN3 | protein | 475 | 70% helix, 2% strand | P40016 |
| P | 26S proteasome regulatory subunit RPN5 | protein | 440 | 73% helix, 3% strand | Q12250 |
| Q | 26S proteasome regulatory subunit RPN6 | protein | 434 | 71% helix, 2% strand | Q12377 |
| R | 26S proteasome regulatory subunit RPN7 | protein | 405 | 71% helix, 3% strand | Q06103 |
| U | 26S proteasome regulatory subunit RPN8 | protein | 290 | 47% helix, 20% strand | Q08723 |
| O | 26S proteasome regulatory subunit RPN9 | protein | 388 | 72% helix, 4% strand | Q04062 |
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 | 655 | 0.86 | 0.90 | 78 | empty |
| 2 | 920 | 0.83 | 0.85 | 124 | empty |
| 3 | 491 | 0.83 | 0.89 | 70 | empty |
| 4 | 614 | 0.79 | 0.84 | 53 | empty |
| 5 | 899 | 0.78 | 0.81 | 87 | empty |
Interfaces
125 interfaces between chains.
- V–U · 3873 Ų buried · 36 hydrogen bonds · protein-protein
- Y–S · 2789 Ų buried · 28 hydrogen bonds · protein-protein
- T–S · 2384 Ų buried · 14 hydrogen bonds · protein-protein
- U–O · 2098 Ų buried · 17 hydrogen bonds · protein-protein
- 2–3 · 1796 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7QO3 · Structure of the 26S proteasome-Ubp6 complex in the si state (Core Particle and Lid) · the same entry in another collection · chain k against k, 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 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
- Elsewhere: RCSB PDB 7QO3 · PDBe 7QO3 · 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
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