MolNFT v1 · #181537 · protein
Structure of human 20S proteasome with bound mpi-5
7LXV · Proteasome subunit alpha type-2: “Structure of human 20S proteasome with bound mpi-5”. Electron microscopy, 1 ligand (YHD), 20 pockets (best druggability 0.79). MolNFT v1 #181537 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7LXV
- Type
- protein
- Length
- 6,204 residues
- Chains
- 28
- Method
- electron microscopy
- 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, Q99436, P49720, P49721, P28074, P20618, P28070, P28072
- Ligands
- YHD
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 14 distinct chains · 35% helix, 30% 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, 27% strand | P25787 |
| B, P | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 239 | 38% helix, 28% strand | P25789 |
| C, Q | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 235 | 40% helix, 26% strand | O14818 |
| D, R | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 236 | 33% helix, 26% strand | P28066 |
| E, S | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 236 | 38% helix, 27% strand | P25786 |
| F, T | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 239 | 38% helix, 27% strand | P25788 |
| G, U | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 242 | 39% helix, 26% strand | P60900 |
| H, V | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 220 | 30% helix, 35% strand | Q99436 |
| I, W | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 32% helix, 30% strand | P49720 |
| J, X | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 196 | 34% helix, 37% strand | P49721 |
| K, Y | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 199 | 36% helix, 36% strand | P28074 |
| L, Z | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 213 | 31% helix, 34% strand | P20618 |
| M, a | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 212 | 35% helix, 35% strand | P28070 |
| N, b | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 202 | 36% helix, 34% strand | P28072 |
Ligands and binding sites
- YHD · N-[(1R)-2-([1,1'-biphenyl]-4-yl)-1-boronoethyl]-1-methyl-L-prolinamide · ligand · 2 copies · chains 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 | 953 | 0.79 | 0.81 | 105 | empty |
| 2 | 1145 | 0.79 | 0.81 | 154 | YHD |
| 3 | 882 | 0.79 | 0.81 | 100 | empty |
| 4 | 754 | 0.78 | 0.82 | 76 | empty |
| 5 | 1005 | 0.77 | 0.79 | 108 | empty |
Interfaces
84 interfaces between chains.
- V–W · 1693 Ų buried · 27 hydrogen bonds · protein-protein
- H–I · 1688 Ų buried · 26 hydrogen bonds · protein-protein
- P–Q · 1544 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1538 Ų buried · 15 hydrogen bonds · protein-protein
- Q–R · 1529 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7LXV · Structure of human 20S proteasome with bound MPI-5 · the same entry in another collection · chain K against K, 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 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
- Every structure of UniProt P28072
- Elsewhere: RCSB PDB 7LXV · PDBe 7LXV · UniProt P25787 · UniProt P25789 · UniProt O14818 · UniProt P28066 · UniProt P25786 · UniProt P25788 · UniProt P60900 · UniProt Q99436 · UniProt P49720 · UniProt P49721 · UniProt P28074 · UniProt P20618 · UniProt P28070 · UniProt P28072
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