Research workbench
Crystal structure of the mammalian 20S proteasome at 2.75 a resolution
Analyse Crystal structure of the mammalian 20S proteasome at 2.75 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IRU
- Type
- protein
- Length
- 6,286 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 20S proteasome
- UniProt
- P33672
- Ligands
- MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 14 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | 20S proteasome | protein | 244 | 37% helix, 26% strand | — |
| B, P | 20S proteasome | protein | 233 | 34% helix, 24% strand | — |
| C, Q | 20S proteasome | protein | 250 | 32% helix, 23% strand | — |
| D, R | 20S proteasome | protein | 243 | 32% helix, 21% strand | — |
| E, S | 20S proteasome | protein | 234 | 32% helix, 26% strand | — |
| F, T | 20S proteasome | protein | 238 | 36% helix, 26% strand | — |
| G, U | 20S proteasome | protein | 245 | 36% helix, 26% strand | — |
| H, V | 20S proteasome | protein | 202 | 35% helix, 34% strand | — |
| I, W | 20S proteasome | protein | 220 | 29% helix, 30% strand | — |
| J, X | 20S proteasome | protein | 204 | 31% helix, 30% strand | P33672 |
| K, Y | 20S proteasome | protein | 199 | 33% helix, 33% strand | — |
| L, Z | 20S proteasome | protein | 201 | 35% helix, 33% strand | — |
| M, 1 | 20S proteasome | protein | 213 | 31% helix, 34% strand | — |
| N, 2 | 20S proteasome | protein | 217 | 33% helix, 33% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 30 copies · chains A, B, C, D, G, I, 1, J, Z, K, M, N, O, P, Q, R, U, W, L, X, Y, 2
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 | 852 | 0.81 | 0.83 | 117 | MG |
| 2 | 979 | 0.80 | 0.82 | 99 | empty |
| 3 | 1164 | 0.80 | 0.81 | 137 | empty |
| 4 | 952 | 0.79 | 0.81 | 96 | empty |
| 5 | 1166 | 0.79 | 0.81 | 128 | MG |
Interfaces
86 interfaces between chains.
- W–X · 1568 Ų buried · 26 hydrogen bonds · protein-protein
- I–J · 1565 Ų buried · 26 hydrogen bonds · protein-protein
- Q–R · 1447 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1444 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1422 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1IRU · Crystal Structure of the mammalian 20S proteasome at 2.75 A resolution · the same entry in another collection · chain A against A, 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 P33672
- Elsewhere: RCSB PDB 1IRU · PDBe 1IRU · UniProt P33672
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