Research workbench
Cryo-EM structure of the PRE3-1 20S proteasome core particle
Analyse Cryo-EM structure of the PRE3-1 20S proteasome core particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LS5
- Type
- protein
- Length
- 6,315 residues
- Chains
- 28
- 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
- UniProt
- P21243, P23639, P23638, P40303, P32379, P40302, P21242, P38624, P25043, P25451, P22141, P30656, P23724, P30657
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 21 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 243 | 40% helix, 22% strand | P21243 |
| B | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 250 | 37% helix, 27% strand | P23639 |
| C | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 239 | 38% helix, 26% strand | P23638 |
| D | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 237 | 38% helix, 24% strand | P40303 |
| E | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 235 | 38% helix, 27% strand | P32379 |
| F, T | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 231 | 35% helix, 26% strand | P40302 |
| G | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 244 | 40% helix, 26% strand | P21242 |
| H, V | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 196 | 36% helix, 35% strand | P38624 |
| I, W | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 220 | 30% helix, 36% strand | P25043 |
| J | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 32% helix, 31% strand | P25451 |
| K, Y | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 194 | 34% helix, 34% strand | P22141 |
| L, Z | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 212 | 36% helix, 32% strand | P30656 |
| M, 1 | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 222 | 29% helix, 30% strand | P23724 |
| N, 2 | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 233 | 33% helix, 30% strand | P30657 |
| O | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 240 | 42% helix, 23% strand | P21243 |
| P | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 246 | 37% helix, 27% strand | P23639 |
| Q | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 244 | 38% helix, 26% strand | P23638 |
| R | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 235 | 39% helix, 24% strand | P40303 |
| S | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 236 | 38% helix, 27% strand | P32379 |
| U | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 243 | 40% helix, 26% strand | P21242 |
| X | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 203 | 33% helix, 32% strand | P25451 |
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 | 930 | 0.82 | 0.84 | 126 | empty |
| 2 | 1037 | 0.81 | 0.82 | 118 | empty |
| 3 | 1008 | 0.80 | 0.82 | 108 | empty |
| 4 | 712 | 0.79 | 0.83 | 88 | empty |
| 5 | 1018 | 0.77 | 0.79 | 108 | empty |
Interfaces
88 interfaces between chains.
- I–J · 1709 Ų buried · 25 hydrogen bonds · protein-protein
- W–X · 1695 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1652 Ų buried · 19 hydrogen bonds · protein-protein
- Q–R · 1533 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1513 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7LS5 · Cryo-EM structure of the Pre3-1 20S proteasome core particle · 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 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
- Elsewhere: RCSB PDB 7LS5 · PDBe 7LS5 · 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
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