Research workbench
Human immunoproteasome 20S particle in complex with compound 1
Analyse Human immunoproteasome 20S particle in complex with compound 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E5B
- Type
- protein
- Length
- 6,207 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit alpha type-2; Proteasome subunit alpha type-4; Proteasome subunit…
- EC
- 3.4.25.1
- UniProt
- P25787, P25789, O14818, P28066, P25786, P25788, P60900, P40306, P49720, P49721, P28062, P20618, P28070, P28065
- Ligands
- HUJ, NA, SCN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 20 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 229 | 36% helix, 28% strand | P25787 |
| B | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 245 | 40% helix, 25% strand | P25789 |
| C | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 227 | 40% helix, 26% strand | O14818 |
| D | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 230 | 34% helix, 26% strand | P28066 |
| E, S | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 236 | 34% helix, 25% strand | P25786 |
| F | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 244 | 36% helix, 24% strand | P25788 |
| G | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 241 | 37% helix, 25% strand | P60900 |
| H, V | Proteasome subunit beta type-10 (EC 3.4.25.1) | protein | 218 | 30% helix, 34% strand | P40306 |
| I, W | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 30% helix, 31% strand | P49720 |
| J | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 196 | 35% helix, 34% strand | P49721 |
| K, Y | Proteasome subunit beta type-8 (EC 3.4.25.1) | protein | 203 | 36% helix, 33% strand | P28062 |
| L, Z | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 213 | 31% helix, 33% strand | P20618 |
| M, a | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 214 | 35% helix, 34% strand | P28070 |
| N, b | Proteasome subunit beta type-9 (EC 3.4.25.1) | protein | 199 | 34% helix, 30% strand | P28065 |
| P | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 246 | 39% helix, 25% strand | P25789 |
| Q | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 234 | 41% helix, 25% strand | O14818 |
| R | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 232 | 34% helix, 25% strand | P28066 |
| T | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 241 | 36% helix, 24% strand | P25788 |
| U | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 242 | 37% helix, 25% strand | P60900 |
| X | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 197 | 35% helix, 34% strand | P49721 |
Ligands and binding sites
- HUJ · [(1R)-3-methyl-1-[[1-[2-[(2,3,4-trimethoxyphenyl) carbonylamino]ethyl]-1,2,3-triazol-4-yl]carbonylamino]butyl]-tris(oxidanyl)boron · ligand · 4 copies · chains K, N, Y, b
- NA · Sodium ion · metal · 12 copies · chains G, H, Z, I, Y, K, W, L, V, N, U, b
- SCN · Thiocyanate ion · ion · 3 copies · chains E, K, L, 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 | 948 | 0.80 | 0.82 | 102 | empty |
| 2 | 1047 | 0.80 | 0.81 | 101 | empty |
| 3 | 1119 | 0.79 | 0.81 | 134 | SCN |
| 4 | 1131 | 0.79 | 0.81 | 117 | empty |
| 5 | 1154 | 0.77 | 0.79 | 127 | HUJ, SCN |
Interfaces
87 interfaces between chains.
- H–I · 1693 Ų buried · 28 hydrogen bonds · protein-protein
- V–W · 1648 Ų buried · 26 hydrogen bonds · protein-protein
- O–P · 1573 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1557 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1532 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6E5B · Human Immunoproteasome 20S particle in complex with compound 1 · the same entry in another collection · chain I against I, 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 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 P60900
- Every structure of UniProt P40306
- Every structure of UniProt P49720
- Every structure of UniProt P49721
- Every structure of UniProt P28062
- Every structure of UniProt P20618
- Every structure of UniProt P28070
- Every structure of UniProt P28065
- Elsewhere: RCSB PDB 6E5B · PDBe 6E5B · UniProt P25787 · UniProt P25789 · UniProt O14818 · UniProt P28066 · UniProt P25786 · UniProt P25788 · UniProt P60900 · UniProt P40306 · UniProt P49720 · UniProt P49721 · UniProt P28062 · UniProt P20618 · UniProt P28070 · UniProt P28065
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