Research workbench
Cryo-EM structure of human immunoproteasome with a novel noncompetitive inhibitor that selectively inhibits activated lymphocytes
Analyse Cryo-EM structure of human immunoproteasome with a novel noncompetitive… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AVO
- Type
- protein
- Length
- 6,192 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit beta type-9; Proteasome subunit beta type-10; Proteasome subunit beta…
- EC
- 3.4.25.1
- UniProt
- P28065, P40306, P28062, P25786, P28066, O14818, P25788, P60900, P25789, P25787, P20618, P49721, P49720, P28070
- Ligands
- BZ7
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 14 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Proteasome subunit beta type-9 (EC 3.4.25.1) | protein | 199 | 34% helix, 25% strand | P28065 |
| B, E | Proteasome subunit beta type-10 (EC 3.4.25.1) | protein | 219 | 30% helix, 26% strand | P40306 |
| C, D | Proteasome subunit beta type-8 (EC 3.4.25.1) | protein | 201 | 35% helix, 29% strand | P28062 |
| G, L | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 234 | 31% helix, 24% strand | P25786 |
| H, M | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 233 | 32% helix, 23% strand | P28066 |
| I, N | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 232 | 37% helix, 22% strand | O14818 |
| J, Q | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 239 | 36% helix, 23% strand | P25788 |
| K, R | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 240 | 34% helix, 23% strand | P60900 |
| O, Z | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 240 | 36% helix, 24% strand | P25789 |
| P, b | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 230 | 35% helix, 22% strand | P25787 |
| S, X | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 213 | 31% helix, 29% strand | P20618 |
| T, V | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 196 | 33% helix, 32% strand | P49721 |
| U, Y | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 32% helix, 26% strand | P49720 |
| W, a | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 216 | 34% helix, 30% strand | P28070 |
Ligands and binding sites
- BZ7 · N~1~-{2-[([1,1'-biphenyl]-3-carbonyl)amino]ethyl}-N~4~-tert-butyl-N~2~-(3-phenylpropanoyl)-L-aspartamide · ligand · 2 copies · chains C, X, D, S
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 | 1073 | 0.80 | 0.81 | 105 | empty |
| 2 | 731 | 0.80 | 0.84 | 81 | empty |
| 3 | 924 | 0.79 | 0.81 | 87 | empty |
| 4 | 1041 | 0.79 | 0.81 | 136 | BZ7 |
| 5 | 742 | 0.79 | 0.83 | 81 | empty |
Interfaces
86 interfaces between chains.
- N–O · 1505 Ų buried · 21 hydrogen bonds · protein-protein
- I–Z · 1468 Ų buried · 20 hydrogen bonds · protein-protein
- E–U · 1465 Ų buried · 21 hydrogen bonds · protein-protein
- B–Y · 1457 Ų buried · 23 hydrogen bonds · protein-protein
- Z–b · 1433 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6AVO · Cryo-EM structure of human immunoproteasome with a novel noncompetitive inhibitor that… · the same entry in another collection · chain S against S, 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 P28065
- Every structure of UniProt P40306
- Every structure of UniProt P28062
- Every structure of UniProt P25786
- Every structure of UniProt P28066
- Every structure of UniProt O14818
- Every structure of UniProt P25788
- Every structure of UniProt P60900
- Every structure of UniProt P25789
- Every structure of UniProt P25787
- Every structure of UniProt P20618
- Every structure of UniProt P49721
- Every structure of UniProt P49720
- Every structure of UniProt P28070
- Elsewhere: RCSB PDB 6AVO · PDBe 6AVO · UniProt P28065 · UniProt P40306 · UniProt P28062 · UniProt P25786 · UniProt P28066 · UniProt O14818 · UniProt P25788 · UniProt P60900 · UniProt P25789 · UniProt P25787 · UniProt P20618 · UniProt P49721 · UniProt P49720 · UniProt P28070
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