MolNFT v1 · #173333 · protein
Human immunoproteasome 20S particle in complex with [(1R)-2-(1- benzofuran-3-yl)-1-{[(1S,2R,4R)-7-OXABICYCLO[2.2.1]HEPTAN-2- YL]FORMAMIDO}ETHYL]BORONIC acid
7AWE · Proteasome subunit alpha type-6: “Human immunoproteasome 20S particle in complex with [(1R)-2-(1…”. X-ray diffraction, 3 ligands (S5K, NA, SCN), 20 pockets (best druggability 0.80). MolNFT v1 #173333 on GenesisL1: 3D structure…
- PDB
- 7AWE
- Type
- protein
- Length
- 6,217 residues
- Chains
- 28
- Method
- x-ray diffraction
- 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, P28065, P40306, P49720, P49721, P28062, P20618, P28070
- Ligands
- S5K, NA, SCN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 21 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteasome subunit alpha type-6 | protein | 240 | 40% helix, 26% strand | P60900 |
| B, P | Proteasome subunit alpha type-2 | protein | 229 | 36% helix, 27% strand | P25787 |
| C | Proteasome subunit alpha type-4 | protein | 243 | 40% helix, 27% strand | P25789 |
| D | Proteasome subunit alpha type-7 | protein | 227 | 40% helix, 26% strand | O14818 |
| E | Proteasome subunit alpha type-5 | protein | 230 | 34% helix, 27% strand | P28066 |
| F | Proteasome subunit alpha type-1 | protein | 236 | 37% helix, 26% strand | P25786 |
| G | Proteasome subunit alpha type-3 | protein | 242 | 37% helix, 27% strand | P25788 |
| H, V | Proteasome subunit beta type-9 (EC 3.4.25.1) | protein | 199 | 35% helix, 32% strand | P28065 |
| I, W | Proteasome subunit beta type-10 (EC 3.4.25.1) | protein | 223 | 29% helix, 35% strand | P40306 |
| J, X | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 30% helix, 31% strand | P49720 |
| K | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 196 | 34% helix, 35% strand | P49721 |
| L, Z | Proteasome subunit beta type-8 (EC 3.4.25.1) | protein | 203 | 37% helix, 35% strand | P28062 |
| M, a | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 213 | 31% helix, 33% strand | P20618 |
| N, b | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 214 | 35% helix, 34% strand | P28070 |
| O | Proteasome subunit alpha type-6 | protein | 242 | 39% helix, 26% strand | P60900 |
| Q | Proteasome subunit alpha type-4 | protein | 253 | 41% helix, 26% strand | P25789 |
| R | Proteasome subunit alpha type-7 | protein | 234 | 41% helix, 25% strand | O14818 |
| S | Proteasome subunit alpha type-5 | protein | 232 | 34% helix, 28% strand | P28066 |
| T | Proteasome subunit alpha type-1 | protein | 235 | 38% helix, 26% strand | P25786 |
| U | Proteasome subunit alpha type-3 | protein | 240 | 37% helix, 27% strand | P25788 |
| Y | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 197 | 34% helix, 35% strand | P49721 |
Ligands and binding sites
- S5K · [(1R)-2-(1-benzofuran-3-yl)-1-{[(1S,2R,4R)-7-oxabicyclo[2.2.1]heptan-2-yl]formamido}ethyl]boronic acid · ligand · 4 copies · chains H, L, M, V, Z, a
- NA · Sodium ion · metal · 13 copies · chains A, H, I, a, J, Z, L, X, M, O, V, W
- SCN · Thiocyanate ion · ion · 11 copies · chains F, D, K, Y, Z, L, M, T, a, U, b, 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 | 1165 | 0.80 | 0.81 | 112 | empty |
| 2 | 1007 | 0.79 | 0.81 | 125 | NA, S5K, SCN |
| 3 | 1088 | 0.79 | 0.81 | 98 | empty |
| 4 | 985 | 0.79 | 0.80 | 97 | empty |
| 5 | 1111 | 0.78 | 0.80 | 106 | empty |
Interfaces
86 interfaces between chains.
- W–X · 1682 Ų buried · 27 hydrogen bonds · protein-protein
- I–J · 1672 Ų buried · 26 hydrogen bonds · protein-protein
- P–Q · 1516 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1512 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1493 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7AWE · HUMAN IMMUNOPROTEASOME 20S PARTICLE IN COMPLEX WITH… · 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 P28065
- 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
- Elsewhere: RCSB PDB 7AWE · PDBe 7AWE · UniProt P60900 · UniProt P25787 · UniProt P25789 · UniProt O14818 · UniProt P28066 · UniProt P25786 · UniProt P25788 · UniProt P28065 · UniProt P40306 · UniProt P49720 · UniProt P49721 · UniProt P28062 · UniProt P20618 · UniProt P28070
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