MolNFT v1 · #125909 · protein
The human 26S proteasome at 6.8 ang.
5LN3 · 26S proteasome non-ATPase regulatory subunit 2: “The human 26S proteasome at 6.8 ang.”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #125909 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LN3
- Type
- protein
- Length
- 9,937 residues
- Chains
- 32
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 26S proteasome non-ATPase regulatory subunit 2; Proteasome subunit beta type-6…
- EC
- 3.4.25.1, 3.4.19.-
- UniProt
- Q13200, P28072, Q99436, P49720, P49721, P28074, P20618, P28070, P60900, P25787, P25789, O14818, P28066, P25786, P25788, P35998, P62191, P62195, P43686, P62333, P17980, Q99460, Q9UNM6, O00232, O00231, Q15008, O43242, P48556, P51665, O00487, P55036, P60896
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 32 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z | 26S proteasome non-ATPase regulatory subunit 2 | protein | 794 | 60% helix, 2% strand | Q13200 |
| 1 | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 214 | 30% helix, 29% strand | P28072 |
| 2 | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 222 | 31% helix, 32% strand | Q99436 |
| 3 | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 205 | 31% helix, 30% strand | P49720 |
| 4 | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 194 | 34% helix, 30% strand | P49721 |
| 5 | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 195 | 34% helix, 29% strand | P28074 |
| 6 | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 213 | 30% helix, 32% strand | P20618 |
| 7 | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 218 | 30% helix, 32% strand | P28070 |
| A | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 239 | 36% helix, 22% strand | P60900 |
| B | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 234 | 36% helix, 21% strand | P25787 |
| C | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 261 | 42% helix, 19% strand | P25789 |
| D | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 248 | 43% helix, 23% strand | O14818 |
| E | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 232 | 34% helix, 24% strand | P28066 |
| F | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 233 | 39% helix, 24% strand | P25786 |
| G | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 242 | 38% helix, 29% strand | P25788 |
| H | 26S protease regulatory subunit 7 | protein | 378 | 40% helix, 8% strand | P35998 |
| I | 26S protease regulatory subunit 4 | protein | 362 | 41% helix, 16% strand | P62191 |
| J | 26S protease regulatory subunit 8 | protein | 373 | 44% helix, 16% strand | P62195 |
| K | 26S protease regulatory subunit 6B | protein | 379 | 41% helix, 16% strand | P43686 |
| L | 26S protease regulatory subunit 10B | protein | 361 | 42% helix, 16% strand | P62333 |
| M | 26S protease regulatory subunit 6A | protein | 389 | 38% helix, 14% strand | P17980 |
| N | 26S proteasome non-ATPase regulatory subunit 1 | protein | 836 | 63% helix, 3% strand | Q99460 |
| O | 26S proteasome non-ATPase regulatory subunit 13 | protein | 376 | 61% helix, 3% strand | Q9UNM6 |
| P | 26S proteasome non-ATPase regulatory subunit 12 | protein | 422 | 69% helix, 3% strand | O00232 |
| Q | 26S proteasome non-ATPase regulatory subunit 11 | protein | 422 | 75% helix, 2% strand | O00231 |
| R | 26S proteasome non-ATPase regulatory subunit 6 | protein | 374 | 71% helix, 2% strand | Q15008 |
| S | 26S proteasome non-ATPase regulatory subunit 3 | protein | 338 | 64% helix, 3% strand | O43242 |
| T | 26S proteasome non-ATPase regulatory subunit 8 | protein | 253 | 66% helix, 3% strand | P48556 |
| U | 26S proteasome non-ATPase regulatory subunit 7 | protein | 272 | 49% helix, 15% strand | P51665 |
| V | 26S proteasome non-ATPase regulatory subunit 14 (EC 3.4.19.-) | protein | 252 | 50% helix, 17% strand | O00487 |
| W | 26S proteasome non-ATPase regulatory subunit 4 | protein | 185 | 35% helix, 21% strand | P55036 |
| Y | 26S proteasome complex subunit DSS1 | protein | 21 | 57% helix, 0% strand | P60896 |
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 | 632 | 0.86 | 0.90 | 77 | empty |
| 2 | 1166 | 0.84 | 0.85 | 97 | empty |
| 3 | 197 | 0.82 | 0.96 | 37 | empty |
| 4 | 164 | 0.81 | 0.96 | 30 | empty |
| 5 | 1054 | 0.81 | 0.82 | 120 | empty |
Interfaces
109 interfaces between chains.
- L–M · 4425 Ų buried · 51 hydrogen bonds · protein-protein
- H–I · 4023 Ų buried · 36 hydrogen bonds · protein-protein
- U–V · 3485 Ų buried · 20 hydrogen bonds · protein-protein
- J–K · 3370 Ų buried · 36 hydrogen bonds · protein-protein
- K–L · 3039 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5LN3 · The human 26S Proteasome at 6.8 Ang. · the same entry in another collection · chain B against B, 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 Q13200
- Every structure of UniProt P28072
- Every structure of UniProt Q99436
- Every structure of UniProt P49720
- Every structure of UniProt P49721
- Every structure of UniProt P28074
- Every structure of UniProt P20618
- Every structure of UniProt P28070
- Every structure of UniProt P60900
- Every structure of UniProt P25787
- Every structure of UniProt P25789
- Every structure of UniProt O14818
- Every structure of UniProt P28066
- Every structure of UniProt P25786
- Every structure of UniProt P25788
- Every structure of UniProt P35998
- Every structure of UniProt P62191
- Every structure of UniProt P62195
- Every structure of UniProt P43686
- Every structure of UniProt P62333
- Every structure of UniProt P17980
- Every structure of UniProt Q99460
- Every structure of UniProt Q9UNM6
- Every structure of UniProt O00232
- Every structure of UniProt O00231
- Every structure of UniProt Q15008
- Every structure of UniProt O43242
- Every structure of UniProt P48556
- Every structure of UniProt P51665
- Every structure of UniProt O00487
- Every structure of UniProt P55036
- Every structure of UniProt P60896
- Elsewhere: RCSB PDB 5LN3 · PDBe 5LN3 · UniProt Q13200 · UniProt P28072 · UniProt Q99436 · UniProt P49720 · UniProt P49721 · UniProt P28074 · UniProt P20618 · UniProt P28070 · UniProt P60900 · UniProt P25787 · UniProt P25789 · UniProt O14818 · UniProt P28066 · UniProt P25786 · UniProt P25788 · UniProt P35998 · UniProt P62191 · UniProt P62195 · UniProt P43686 · UniProt P62333 · UniProt P17980 · UniProt Q99460 · UniProt Q9UNM6 · UniProt O00232 · UniProt O00231 · UniProt Q15008 · UniProt O43242 · UniProt P48556 · UniProt P51665 · UniProt O00487 · UniProt P55036 · UniProt P60896
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