Research workbench
Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core
Analyse Cryo-EM reveals the conformation of a substrate analogue in the human 20S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A0Q
- Type
- protein
- Length
- 5,582 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit alpha type-6; Proteasome subunit alpha type-2; Proteasome subunit…
- EC
- 3.4.25.1
- UniProt
- P60900, P25787, P25789, O14818, P28066, P25786, P25788, P28072, Q99436, P49720, P49721, P28074, P20618, P28070
- Ligands
- KNM
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 14 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 195 | 36% helix, 26% strand | P60900 |
| B, P | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 214 | 33% helix, 23% strand | P25787 |
| C, Q | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 237 | 38% helix, 24% strand | P25789 |
| D, R | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 214 | 33% helix, 19% strand | O14818 |
| E, S | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 215 | 33% helix, 23% strand | P28066 |
| F, T | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 195 | 37% helix, 25% strand | P25786 |
| G, U | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 209 | 39% helix, 19% strand | P25788 |
| H, V | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 183 | 33% helix, 17% strand | P28072 |
| I, W | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 198 | 31% helix, 33% strand | Q99436 |
| J, X | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 176 | 32% helix, 27% strand | P49720 |
| K, Y | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 189 | 34% helix, 31% strand | P49721 |
| L, Z | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 192 | 32% helix, 24% strand | P28074 |
| M, a | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 190 | 34% helix, 23% strand | P20618 |
| N, b | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 184 | 31% helix, 29% strand | P28070 |
Ligands and binding sites
- KNM · Ada-(ahx)3-(leu)3-vinyl sulfone · ligand · 6 copies · chains H, I, J, L, M, V, W, X, Z, a
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 | 974 | 0.77 | 0.79 | 90 | empty |
| 2 | 974 | 0.76 | 0.79 | 91 | empty |
| 3 | 936 | 0.76 | 0.78 | 95 | empty |
| 4 | 613 | 0.75 | 0.82 | 76 | empty |
| 5 | 862 | 0.74 | 0.78 | 80 | empty |
Interfaces
80 interfaces between chains.
- A–B · 1374 Ų buried · 15 hydrogen bonds · protein-protein
- O–P · 1374 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1349 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1343 Ų buried · 20 hydrogen bonds · protein-protein
- P–Q · 1342 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 5A0Q · Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core · the same entry in another collection · chain J against J, 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 P60900
- Every structure of UniProt P25787
- Every structure of UniProt P25789
- Every structure of UniProt O14818
- Every structure of UniProt P28066
- Every structure of UniProt P25786
- Every structure of UniProt P25788
- Every structure of UniProt P28072
- Every structure of UniProt Q99436
- Every structure of UniProt P49720
- Every structure of UniProt P49721
- Every structure of UniProt P28074
- Every structure of UniProt P20618
- Every structure of UniProt P28070
- Elsewhere: RCSB PDB 5A0Q · PDBe 5A0Q · UniProt P60900 · UniProt P25787 · UniProt P25789 · UniProt O14818 · UniProt P28066 · UniProt P25786 · UniProt P25788 · UniProt P28072 · UniProt Q99436 · UniProt P49720 · UniProt P49721 · UniProt P28074 · UniProt P20618 · UniProt P28070
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