MolNFT v1 · #113102 · protein
Structure of the 26S proteasome-UBP6 complex
5A5B · Proteasome component PRE3: “Structure of the 26S proteasome-UBP6 complex”. Electron microscopy, 1 ligand (MSE), 20 pockets (best druggability 0.86). MolNFT v1 #113102 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5A5B
- Type
- protein
- Length
- 10,609 residues
- Chains
- 35
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome component PRE3; Proteasome component PUP1; Proteasome component PUP3…
- EC
- 3.4.25.1, 3.1.2.15
- UniProt
- P38624, P25043, P25451, P22141, P30656, P23724, P30657, P43593, P0CG48, P21243, P23639, P23638, P40303, P32379, P40302, P21242, P33299, P40327, Q01939, P33298, P53549, P33297, P32565, Q04062, Q12250, Q12377, Q06103, P40016, P32496, Q08723, P43588, P38886, O13563, O94742, P38764
- Ligands
- MSE
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 35 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Proteasome component PRE3 (EC 3.4.25.1) | protein | 205 | 33% helix, 33% strand | P38624 |
| 2 | Proteasome component PUP1 (EC 3.4.25.1) | protein | 223 | 29% helix, 34% strand | P25043 |
| 3 | Proteasome component PUP3 (EC 3.4.25.1) | protein | 204 | 31% helix, 32% strand | P25451 |
| 4 | Proteasome component C11 (EC 3.4.25.1) | protein | 198 | 33% helix, 32% strand | P22141 |
| 5 | Proteasome component PRE2 (EC 3.4.25.1) | protein | 212 | 35% helix, 34% strand | P30656 |
| 6 | Proteasome component C5 (EC 3.4.25.1) | protein | 222 | 28% helix, 32% strand | P23724 |
| 7 | Proteasome component PRE4 (EC 3.4.25.1) | protein | 233 | 30% helix, 30% strand | P30657 |
| 8 | Ubiquitin carboxyl-terminal hydrolase 6 (EC 3.1.2.15) | protein | 367 | 39% helix, 27% strand | P43593 |
| 9 | Ubiquitin aldehyde | protein | 76 | 20% helix, 33% strand | P0CG48 |
| A | Proteasome component C7-alpha (EC 3.4.25.1) | protein | 243 | 36% helix, 21% strand | P21243 |
| B | Proteasome component Y7 (EC 3.4.25.1) | protein | 250 | 33% helix, 24% strand | P23639 |
| C | Proteasome component Y13 (EC 3.4.25.1) | protein | 245 | 34% helix, 22% strand | P23638 |
| D | Proteasome component PRE6 (EC 3.4.25.1) | protein | 242 | 37% helix, 24% strand | P40303 |
| E | Proteasome component PUP2 (EC 3.4.25.1) | protein | 243 | 34% helix, 26% strand | P32379 |
| F | Proteasome component PRE5 (EC 3.4.25.1) | protein | 233 | 38% helix, 27% strand | P40302 |
| G | Proteasome component C1 (EC 3.4.25.1) | protein | 245 | 38% helix, 26% strand | P21242 |
| H | 26S protease regulatory subunit 7 homolog | protein | 359 | 40% helix, 9% strand | P33299 |
| I | 26S protease regulatory subunit 4 homolog | protein | 362 | 42% helix, 15% strand | P40327 |
| J | 26S protease regulatory subunit 8 homolog | protein | 373 | 43% helix, 18% strand | Q01939 |
| K | 26S protease regulatory subunit 6B homolog | protein | 381 | 42% helix, 17% strand | P33298 |
| L | 26S protease subunit RPT4 | protein | 361 | 43% helix, 17% strand | P53549 |
| M | 26S protease regulatory subunit 6A | protein | 367 | 41% helix, 15% strand | P33297 |
| N | 26S proteasome regulatory subunit RPN2 | protein | 849 | 62% helix, 3% strand | P32565 |
| O | 26S proteasome regulatory subunit RPN9 | protein | 387 | 63% helix, 2% strand | Q04062 |
| P | 26S proteasome regulatory subunit RPN5 | protein | 415 | 73% helix, 3% strand | Q12250 |
| Q | 26S proteasome regulatory subunit RPN6 | protein | 431 | 73% helix, 3% strand | Q12377 |
| R | 26S proteasome regulatory subunit RPN7 | protein | 400 | 65% helix, 3% strand | Q06103 |
| S | 26S proteasome regulatory subunit RPN3 | protein | 353 | 61% helix, 2% strand | P40016 |
| T | 26S proteasome regulatory subunit RPN12 | protein | 272 | 66% helix, 2% strand | P32496 |
| U | 26S proteasome regulatory subunit RPN8 | protein | 255 | 46% helix, 17% strand | Q08723 |
| V | 26S proteasome regulatory subunit RPN11 | protein | 247 | 47% helix, 17% strand | P43588 |
| W | 26S proteasome regulatory subunit RPN10 | protein | 197 | 34% helix, 14% strand | P38886 |
| X | 26S proteasome regulatory subunit RPN13 | protein | 127 | 9% helix, 20% strand | O13563 |
| Y | 26S proteasome complex subunit SEM1 | protein | 19 | 84% helix, 0% strand | O94742 |
| Z | 26S proteasome regulatory subunit RPN1 | protein | 813 | 58% helix, 3% strand | P38764 |
Ligands and binding sites
- MSE · Selenomethionine · ion · chains 8
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 | 1030 | 0.86 | 0.87 | 112 | empty |
| 2 | 1132 | 0.85 | 0.85 | 116 | empty |
| 3 | 643 | 0.83 | 0.88 | 80 | empty |
| 4 | 679 | 0.83 | 0.87 | 60 | empty |
| 5 | 886 | 0.83 | 0.85 | 91 | empty |
Interfaces
117 interfaces between chains.
- L–M · 3951 Ų buried · 34 hydrogen bonds · protein-protein
- H–I · 3543 Ų buried · 52 hydrogen bonds · protein-protein
- J–K · 3160 Ų buried · 27 hydrogen bonds · protein-protein
- U–V · 3123 Ų buried · 23 hydrogen bonds · protein-protein
- K–L · 2793 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered, nonstandard).
Compared structures
- 5A5B · Structure of the 26S proteasome-Ubp6 complex · the same entry in another collection · chain A against A, 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 P43593
- Every structure of UniProt P0CG48
- 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 P32565
- Every structure of UniProt Q04062
- Every structure of UniProt Q12250
- Every structure of UniProt Q12377
- Every structure of UniProt Q06103
- Every structure of UniProt P40016
- Every structure of UniProt P32496
- Every structure of UniProt Q08723
- Every structure of UniProt P43588
- Every structure of UniProt P38886
- Every structure of UniProt O13563
- Every structure of UniProt O94742
- Every structure of UniProt P38764
- Elsewhere: RCSB PDB 5A5B · PDBe 5A5B · UniProt P38624 · UniProt P25043 · UniProt P25451 · UniProt P22141 · UniProt P30656 · UniProt P23724 · UniProt P30657 · UniProt P43593 · UniProt P0CG48 · 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 P32565 · UniProt Q04062 · UniProt Q12250 · UniProt Q12377 · UniProt Q06103 · UniProt P40016 · UniProt P32496 · UniProt Q08723 · UniProt P43588 · UniProt P38886 · UniProt O13563 · UniProt O94742 · UniProt P38764
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