MolNFT v1 · #88317 · protein
Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome
4CR2 · Proteasome component PRE3: “Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #88317 on GenesisL1: 3D…
- PDB
- 4CR2
- Type
- protein
- Length
- 10,166 residues
- Chains
- 33
- 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
- UniProt
- P38624, P25043, P25451, P22141, P30656, P23724, P30657, 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
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 33 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Proteasome component PRE3 (EC 3.4.25.1) | protein | 205 | 35% helix, 33% strand | P38624 |
| 2 | Proteasome component PUP1 (EC 3.4.25.1) | protein | 223 | 29% helix, 35% strand | P25043 |
| 3 | Proteasome component PUP3 (EC 3.4.25.1) | protein | 204 | 31% helix, 31% strand | P25451 |
| 4 | Proteasome component C11 (EC 3.4.25.1) | protein | 198 | 34% helix, 32% strand | P22141 |
| 5 | Proteasome component PRE2 (EC 3.4.25.1) | protein | 212 | 34% helix, 32% strand | P30656 |
| 6 | Proteasome component C5 (EC 3.4.25.1) | protein | 222 | 29% helix, 32% strand | P23724 |
| 7 | Proteasome component PRE4 (EC 3.4.25.1) | protein | 233 | 32% helix, 30% strand | P30657 |
| A | Proteasome component C7-alpha (EC 3.4.25.1) | protein | 243 | 37% 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 | 36% helix, 24% strand | P23638 |
| D | Proteasome component PRE6 (EC 3.4.25.1) | protein | 242 | 38% helix, 24% strand | P40303 |
| E | Proteasome component PUP2 (EC 3.4.25.1) | protein | 243 | 33% helix, 24% strand | P32379 |
| F | Proteasome component PRE5 (EC 3.4.25.1) | protein | 233 | 38% helix, 26% strand | P40302 |
| G | Proteasome component C1 (EC 3.4.25.1) | protein | 245 | 37% helix, 27% strand | P21242 |
| H | 26S protease regulatory subunit 7 homolog | protein | 359 | 41% helix, 10% strand | P33299 |
| I | 26S protease regulatory subunit 4 homolog | protein | 362 | 44% 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 | 41% helix, 17% strand | P33298 |
| L | 26S protease subunit RPT4 | protein | 361 | 42% helix, 16% strand | P53549 |
| M | 26S protease regulatory subunit 6A | protein | 367 | 41% helix, 17% strand | P33297 |
| N | 26S proteasome regulatory subunit RPN2 | protein | 849 | 64% helix, 3% strand | P32565 |
| O | 26S proteasome regulatory subunit RPN9 | protein | 387 | 61% helix, 2% strand | Q04062 |
| P | 26S proteasome regulatory subunit RPN5 | protein | 415 | 72% helix, 3% strand | Q12250 |
| Q | 26S proteasome regulatory subunit RPN6 | protein | 431 | 74% helix, 2% strand | Q12377 |
| R | 26S proteasome regulatory subunit RPN7 | protein | 400 | 65% helix, 3% strand | Q06103 |
| S | 26S proteasome regulatory subunit RPN3 | protein | 353 | 63% helix, 3% strand | P40016 |
| T | 26S proteasome regulatory subunit RPN12 | protein | 272 | 63% helix, 3% strand | P32496 |
| U | 26S proteasome regulatory subunit RPN8 | protein | 255 | 51% helix, 21% strand | Q08723 |
| V | 26S proteasome regulatory subunit RPN11 | protein | 247 | 50% helix, 20% strand | P43588 |
| W | 26S proteasome regulatory subunit RPN10 | protein | 197 | 36% helix, 19% strand | P38886 |
| X | 26S proteasome regulatory subunit RPN13 | protein | 127 | 9% helix, 30% strand | O13563 |
| Y | 26S proteasome complex subunit SEM1 | protein | 19 | 84% helix, 0% strand | O94742 |
| Z | 26S proteasome regulatory subunit RPN1 | protein | 813 | 59% helix, 2% strand | P38764 |
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 | 995 | 0.85 | 0.86 | 83 | empty |
| 2 | 707 | 0.84 | 0.88 | 86 | empty |
| 3 | 1120 | 0.83 | 0.84 | 100 | empty |
| 4 | 690 | 0.81 | 0.86 | 75 | empty |
| 5 | 488 | 0.81 | 0.88 | 54 | empty |
Interfaces
111 interfaces between chains.
- L–M · 3893 Ų buried · 29 hydrogen bonds · protein-protein
- J–K · 3446 Ų buried · 30 hydrogen bonds · protein-protein
- U–V · 3366 Ų buried · 17 hydrogen bonds · protein-protein
- H–I · 3225 Ų buried · 38 hydrogen bonds · protein-protein
- K–L · 3004 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 4CR2 · Deep classification of a large cryo-EM dataset defines the conformational landscape of… · 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 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 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 4CR2 · PDBe 4CR2 · UniProt P38624 · UniProt P25043 · UniProt P25451 · UniProt P22141 · UniProt P30656 · UniProt P23724 · UniProt P30657 · 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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