Research workbench
Crystal structure of the 20S proteasome from yeast at 2.4 ångströms resolution
Analyse Crystal structure of the 20S proteasome from yeast at 2.4 ångströms resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RYP
- Type
- protein
- Length
- 6,386 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 20S proteasome
- EC
- 3.4.99.46
- UniProt
- P21243, P23639, P23638, P40303, P32379, P40302, P21242, P38624, P25043, P25451, P22141, P30656, P23724, P30657
- Ligands
- MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 14 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | 20S proteasome (EC 3.4.99.46) | protein | 243 | 40% helix, 23% strand | P21243 |
| B, P | 20S proteasome (EC 3.4.99.46) | protein | 250 | 35% helix, 26% strand | P23639 |
| C, Q | 20S proteasome (EC 3.4.99.46) | protein | 244 | 38% helix, 25% strand | P23638 |
| D, R | 20S proteasome (EC 3.4.99.46) | protein | 241 | 36% helix, 24% strand | P40303 |
| E, S | 20S proteasome (EC 3.4.99.46) | protein | 242 | 35% helix, 26% strand | P32379 |
| F, T | 20S proteasome (EC 3.4.99.46) | protein | 233 | 38% helix, 27% strand | P40302 |
| G, U | 20S proteasome (EC 3.4.99.46) | protein | 244 | 38% helix, 26% strand | P21242 |
| H, V | 20S proteasome (EC 3.4.99.46) | protein | 205 | 35% helix, 35% strand | P38624 |
| I, W | 20S proteasome (EC 3.4.99.46) | protein | 222 | 29% helix, 34% strand | P25043 |
| J, X | 20S proteasome (EC 3.4.99.46) | protein | 204 | 32% helix, 32% strand | P25451 |
| K, Y | 20S proteasome (EC 3.4.99.46) | protein | 198 | 34% helix, 33% strand | P22141 |
| L, Z | 20S proteasome (EC 3.4.99.46) | protein | 212 | 36% helix, 33% strand | P30656 |
| M, 1 | 20S proteasome (EC 3.4.99.46) | protein | 222 | 28% helix, 32% strand | P23724 |
| N, 2 | 20S proteasome (EC 3.4.99.46) | protein | 233 | 32% helix, 31% strand | P30657 |
Ligands and binding sites
- MG · Magnesium ion · metal · 20 copies · chains A, B, G, E, M, H, 2, I, 1, J, L, X, O, P, U, S, N, V, W, Z
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 | 1083 | 0.84 | 0.85 | 131 | MG |
| 2 | 1071 | 0.80 | 0.81 | 111 | empty |
| 3 | 951 | 0.80 | 0.82 | 103 | empty |
| 4 | 1048 | 0.80 | 0.81 | 116 | MG |
| 5 | 708 | 0.80 | 0.84 | 93 | empty |
Interfaces
92 interfaces between chains.
- W–X · 1700 Ų buried · 28 hydrogen bonds · protein-protein
- I–J · 1681 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1671 Ų buried · 25 hydrogen bonds · protein-protein
- Q–R · 1631 Ų buried · 22 hydrogen bonds · protein-protein
- I–1 · 1495 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1RYP · Crystal structure of the 20S proteasome from yeast at 2.4 ångströms resolution · 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 1RYP · PDBe 1RYP · 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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