Research workbench
Yeast 20S proteasome in complex with the covalently bound inhibitor B- lactone (2R,3S)-3-isopropyl-4-oxo-2-oxetane-carboxylate (ioc)
Analyse Yeast 20S proteasome in complex with the covalently bound inhibitor B- lactone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O2L
- Type
- protein
- Length
- 6,334 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLJ1_G0039880.MRNA.1.CDS.1; BJ4_G0021480.MRNA.1.CDS.1; HLJ1_G0048980.MRNA.1.CDS.1; 20S…
- EC
- 3.4.25.1
- UniProt
- A0A6L1BIF8, A0A6A5PXC6, A0A6A5Q273, P32379, A0A6A5PTH4, A0A6A5Q4M4, A0A6A5PYC9, A0A6A5Q449, A0A6L0YA22, A0A6A5Q0W2, A0A6V8RU78, A0A6A5Q0P3, P30657, A0A6L0ZSP2
- Ligands
- V08, MG, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 14 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | HLJ1_G0039880.MRNA.1.CDS.1 | protein | 250 | 34% helix, 26% strand | A0A6L1BIF8 |
| B, P | BJ4_G0021480.MRNA.1.CDS.1 | protein | 244 | 37% helix, 25% strand | A0A6A5PXC6 |
| C, Q | HLJ1_G0048980.MRNA.1.CDS.1 | protein | 240 | 36% helix, 22% strand | A0A6A5Q273 |
| D, R | 20S proteasome | protein | 235 | 37% helix, 27% strand | P32379 |
| E, S | BJ4_G0043800.MRNA.1.CDS.1 | protein | 231 | 38% helix, 28% strand | A0A6A5PTH4 |
| F, T | Probable proteasome subunit alpha type-7 | protein | 243 | 40% helix, 26% strand | A0A6A5Q4M4 |
| G, U | BJ4_G0020160.MRNA.1.CDS.1 | protein | 241 | 39% helix, 23% strand | A0A6A5PYC9 |
| H, V | Proteasome endopeptidase complex (EC 3.4.25.1) | protein | 226 | 29% helix, 33% strand | A0A6A5Q449 |
| I, W | Proteasome endopeptidase complex (EC 3.4.25.1) | protein | 204 | 32% helix, 33% strand | A0A6L0YA22 |
| J, X | Proteasome subunit beta (EC 3.4.25.1) | protein | 195 | 33% helix, 35% strand | A0A6A5Q0W2 |
| K, Y | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 212 | 36% helix, 35% strand | A0A6V8RU78 |
| L, Z | Proteasome endopeptidase complex (EC 3.4.25.1) | protein | 222 | 28% helix, 32% strand | A0A6A5Q0P3 |
| M, a | Proteasome subunit beta type-7 | protein | 228 | 32% helix, 32% strand | P30657 |
| N, b | Proteasome endopeptidase complex (EC 3.4.25.1) | protein | 196 | 36% helix, 34% strand | A0A6L0ZSP2 |
Ligands and binding sites
- V08 · (2 {R},3 {S})-3-methanoyl-4-methyl-2-hydroxy-pentanoic acid · ligand · 6 copies · chains H, K, N, V, Y, b
- MG · Magnesium ion · metal · 8 copies · chains G, I, Y, K, W, N, a, L, V, H, Z
- CL · Chloride ion · ion · 2 copies · chains G, H, U, V
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 | 1159 | 0.83 | 0.84 | 163 | V08 |
| 2 | 948 | 0.82 | 0.84 | 117 | V08 |
| 3 | 891 | 0.81 | 0.83 | 106 | empty |
| 4 | 708 | 0.80 | 0.84 | 96 | empty |
| 5 | 1011 | 0.79 | 0.81 | 119 | empty |
Interfaces
90 interfaces between chains.
- V–W · 1809 Ų buried · 30 hydrogen bonds · protein-protein
- H–I · 1769 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1612 Ų buried · 27 hydrogen bonds · protein-protein
- P–Q · 1583 Ų buried · 23 hydrogen bonds · protein-protein
- L–V · 1564 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 7O2L · Yeast 20S proteasome in complex with the covalently bound inhibitor b-lactone… · 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
- Every structure of UniProt A0A6L1BIF8
- Every structure of UniProt A0A6A5PXC6
- Every structure of UniProt A0A6A5Q273
- Every structure of UniProt P32379
- Every structure of UniProt A0A6A5PTH4
- Every structure of UniProt A0A6A5Q4M4
- Every structure of UniProt A0A6A5PYC9
- Every structure of UniProt A0A6A5Q449
- Every structure of UniProt A0A6L0YA22
- Every structure of UniProt A0A6A5Q0W2
- Every structure of UniProt A0A6V8RU78
- Every structure of UniProt A0A6A5Q0P3
- Every structure of UniProt P30657
- Every structure of UniProt A0A6L0ZSP2
- Elsewhere: RCSB PDB 7O2L · PDBe 7O2L · UniProt A0A6L1BIF8 · UniProt A0A6A5PXC6 · UniProt A0A6A5Q273 · UniProt P32379 · UniProt A0A6A5PTH4 · UniProt A0A6A5Q4M4 · UniProt A0A6A5PYC9 · UniProt A0A6A5Q449 · UniProt A0A6L0YA22 · UniProt A0A6A5Q0W2 · UniProt A0A6V8RU78 · UniProt A0A6A5Q0P3 · UniProt P30657 · UniProt A0A6L0ZSP2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.