Research workbench
Structure of yeast 20S open-gate proteasome with compound 20
Analyse Structure of yeast 20S open-gate proteasome with compound 20 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SDI
- Type
- protein
- Length
- 6,293 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome component Y7; Proteasome component Y13; Proteasome component PRE6; Proteasome…
- EC
- 3.4.25.1
- UniProt
- P23639, P23638, P40303, P32379, P40302, P21242, P21243, P25043, P25451, P22141, P30656, P23724, P30657, P38624
- Ligands
- 3SD, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 15 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | Proteasome component Y7 (EC 3.4.25.1) | protein | 246 | 35% helix, 26% strand | P23639 |
| B, P | Proteasome component Y13 (EC 3.4.25.1) | protein | 235 | 37% helix, 27% strand | P23638 |
| C, Q | Proteasome component PRE6 (EC 3.4.25.1) | protein | 238 | 37% helix, 24% strand | P40303 |
| D | Proteasome component PUP2 (EC 3.4.25.1) | protein | 228 | 39% helix, 27% strand | P32379 |
| E, S | Proteasome component PRE5 (EC 3.4.25.1) | protein | 230 | 35% helix, 28% strand | P40302 |
| F, T | Proteasome component C1 (EC 3.4.25.1) | protein | 242 | 38% helix, 26% strand | P21242 |
| G, U | Proteasome component C7-alpha (EC 3.4.25.1) | protein | 240 | 39% helix, 23% strand | P21243 |
| H, V | Proteasome component PUP1 (EC 3.4.25.1) | protein | 222 | 29% helix, 35% strand | P25043 |
| I, W | Proteasome component PUP3 (EC 3.4.25.1) | protein | 204 | 33% helix, 33% strand | P25451 |
| J, X | Proteasome component C11 (EC 3.4.25.1) | protein | 198 | 34% helix, 34% strand | P22141 |
| K, Y | Proteasome component PRE2 (EC 3.4.25.1) | protein | 212 | 36% helix, 34% strand | P30656 |
| L, Z | Proteasome component C5 (EC 3.4.25.1) | protein | 222 | 29% helix, 32% strand | P23724 |
| M, 1 | Proteasome component PRE4 (EC 3.4.25.1) | protein | 233 | 31% helix, 31% strand | P30657 |
| N, 2 | Proteasome component PRE3 (EC 3.4.25.1) | protein | 196 | 36% helix, 34% strand | P38624 |
| R | Proteasome component PUP2 (EC 3.4.25.1) | protein | 229 | 39% helix, 27% strand | P32379 |
Ligands and binding sites
- 3SD · N~4~-(2,2-dimethylpropyl)-N~1~-{(2S)-1-[(4-methylbenzyl)amino]-1-oxo-4-phenylbutan-2-yl}-N~2~-[(5-methyl-1,2-oxazol-3-yl)carbonyl]-L-aspartamide · ligand · 2 copies · chains K, L, Y, Z
- MG · Magnesium ion · metal · 20 copies · chains F, G, H, Z, I, K, W, D, L, V, N, 1, T, U, Y, R, M, 2
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains K, Y
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 | 983 | 0.83 | 0.84 | 119 | empty |
| 2 | 915 | 0.82 | 0.84 | 120 | empty |
| 3 | 1086 | 0.81 | 0.82 | 101 | empty |
| 4 | 1046 | 0.81 | 0.82 | 113 | empty |
| 5 | 1124 | 0.80 | 0.82 | 116 | empty |
Interfaces
78 interfaces between chains.
- H–I · 1718 Ų buried · 27 hydrogen bonds · protein-protein
- V–W · 1697 Ų buried · 30 hydrogen bonds · protein-protein
- T–U · 1490 Ų buried · 17 hydrogen bonds · protein-protein
- L–V · 1483 Ų buried · 22 hydrogen bonds · protein-protein
- F–G · 1469 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3SDI · Structure of yeast 20S open-gate proteasome with Compound 20 · 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 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 P21243
- 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 P38624
- Elsewhere: RCSB PDB 3SDI · PDBe 3SDI · UniProt P23639 · UniProt P23638 · UniProt P40303 · UniProt P32379 · UniProt P40302 · UniProt P21242 · UniProt P21243 · UniProt P25043 · UniProt P25451 · UniProt P22141 · UniProt P30656 · UniProt P23724 · UniProt P30657 · UniProt P38624
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