Research workbench
Cryo-EM structure of 13S proteasome core particle assembly intermediate purified from PRE3-1 proteasome mutant (G34D)
Analyse Cryo-EM structure of 13S proteasome core particle assembly intermediate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LSX
- Type
- protein
- Length
- 2,838 residues
- Chains
- 13
- 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, P38293, P25043, P25451, P22141, Q05778, P36040
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 13 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 245 | 41% helix, 23% strand | P21243 |
| B | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 247 | 37% helix, 25% strand | P23639 |
| C | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 234 | 37% helix, 24% strand | P23638 |
| D | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 235 | 35% helix, 21% strand | P40303 |
| E | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 249 | 37% helix, 24% strand | P32379 |
| F | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 234 | 38% helix, 26% strand | P40302 |
| G | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 245 | 37% helix, 24% strand | P21242 |
| H | Proteasome maturation factor UMP1 | protein | 91 | 65% helix, 0% strand | P38293 |
| I | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 207 | 35% helix, 29% strand | P25043 |
| J | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 176 | 32% helix, 28% strand | P25451 |
| K | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 182 | 37% helix, 31% strand | P22141 |
| O | Proteasome chaperone 1 | protein | 240 | 29% helix, 24% strand | Q05778 |
| P | Proteasome assembly chaperone 2 | protein | 253 | 30% helix, 24% strand | P36040 |
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 | 779 | 0.84 | 0.87 | 78 | empty |
| 2 | 806 | 0.83 | 0.86 | 111 | empty |
| 3 | 719 | 0.80 | 0.84 | 62 | empty |
| 4 | 1019 | 0.77 | 0.79 | 90 | empty |
| 5 | 355 | 0.76 | 0.87 | 53 | empty |
Interfaces
40 interfaces between chains.
- O–P · 1866 Ų buried · 19 hydrogen bonds · protein-protein
- E–O · 1543 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1534 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1516 Ų buried · 7 hydrogen bonds · protein-protein
- A–G · 1506 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7LSX · Cryo-EM structure of 13S proteasome core particle assembly intermediate purified from… · the same entry in another collection · chain P against P, 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 P38293
- Every structure of UniProt P25043
- Every structure of UniProt P25451
- Every structure of UniProt P22141
- Every structure of UniProt Q05778
- Every structure of UniProt P36040
- Elsewhere: RCSB PDB 7LSX · PDBe 7LSX · UniProt P21243 · UniProt P23639 · UniProt P23638 · UniProt P40303 · UniProt P32379 · UniProt P40302 · UniProt P21242 · UniProt P38293 · UniProt P25043 · UniProt P25451 · UniProt P22141 · UniProt Q05778 · UniProt P36040
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