MolNFT v1 · #21067 · protein
Crystal structure of the 20S proteasome from yeast at 2.4 ångströms resolution
1RYP: “Crystal structure of the 20S proteasome from yeast at 2.4 ångströms resolution”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.84). MolNFT v1 #21067 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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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