Research workbench
Leishmania tarentolae proteasome 20S subunit complexed with GSK3494245
Analyse Leishmania tarentolae proteasome 20S subunit complexed with GSK3494245 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QM7
- Type
- protein
- Length
- 6,350 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome ALPHA1 chain; Proteasome ALPHA2 chain; Proteasome ALPHA3 chain; Proteasome…
- Ligands
- J6E
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 14 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | Proteasome ALPHA1 chain | protein | 244 | 39% helix, 26% strand | — |
| B, P | Proteasome ALPHA2 chain | protein | 229 | 38% helix, 28% strand | — |
| C, Q | Proteasome ALPHA3 chain | protein | 276 | 38% helix, 25% strand | — |
| D, R | Proteasome ALPHA4 chain | protein | 239 | 38% helix, 24% strand | — |
| E, S | Proteasome ALPHA5 chain | protein | 229 | 35% helix, 28% strand | — |
| F, T | Proteasome ALPHA6 chain | protein | 238 | 34% helix, 27% strand | — |
| G, U | Proteasome ALPHA7 chain | protein | 228 | 32% helix, 27% strand | — |
| H, V | Proteasome BETA1 chain | protein | 229 | 31% helix, 28% strand | — |
| I, W | Proteasome BETA2 chain | protein | 219 | 30% helix, 36% strand | — |
| J, X | Proteasome BETA3 chain | protein | 204 | 30% helix, 34% strand | — |
| K, Y | Proteasome BETA4 chain | protein | 206 | 32% helix, 33% strand | — |
| L, Z | Proteasome BETA5 chain | protein | 202 | 35% helix, 33% strand | — |
| M, a | Proteasome BETA6 chain | protein | 214 | 30% helix, 30% strand | — |
| N, b | Proteasome BETA7 chain | protein | 218 | 36% helix, 30% strand | — |
Ligands and binding sites
- J6E · ~{N}-[4-fluoranyl-3-(3-morpholin-4-ylimidazo[1,2-a]pyrimidin-7-yl)phenyl]pyrrolidine-1-carboxamide · ligand · 2 copies · chains K, L, X, J, Y, 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 | 1149 | 0.83 | 0.85 | 87 | empty |
| 2 | 1114 | 0.83 | 0.84 | 77 | empty |
| 3 | 445 | 0.81 | 0.89 | 44 | empty |
| 4 | 455 | 0.80 | 0.88 | 42 | empty |
| 5 | 960 | 0.79 | 0.81 | 115 | empty |
Interfaces
86 interfaces between chains.
- H–b · 2417 Ų buried · 43 hydrogen bonds · protein-protein
- N–V · 2409 Ų buried · 44 hydrogen bonds · protein-protein
- I–J · 1749 Ų buried · 22 hydrogen bonds · protein-protein
- W–X · 1742 Ų buried · 24 hydrogen bonds · protein-protein
- P–Q · 1580 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6QM7 · Leishmania tarentolae proteasome 20S subunit complexed with GSK3494245 · 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
- Elsewhere: RCSB PDB 6QM7 · PDBe 6QM7
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