MolNFT v1 · #104143 · protein
Yeast 20S proteasome in complex with kendomycin
4Q1S · Proteasome subunit alpha type-2: “Yeast 20S proteasome in complex with kendomycin”. X-ray diffraction, 1 ligand (2YD), 20 pockets (best druggability 0.83). MolNFT v1 #104143 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4Q1S
- Type
- protein
- Length
- 6,367 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-3; Proteasome subunit…
- EC
- 3.4.25.1
- UniProt
- P23639, P23638, P40303, P32379, P40302, P21242, P21243, P25043, P25451, P22141, P30656, P23724, P30657, P38624
- Ligands
- 2YD
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 15 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 250 | 36% helix, 26% strand | P23639 |
| B, P | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 244 | 38% helix, 25% strand | P23638 |
| C, Q | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 241 | 35% helix, 24% strand | P40303 |
| D, R | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 242 | 36% helix, 26% strand | P32379 |
| E, S | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 233 | 36% helix, 27% strand | P40302 |
| F, T | Probable proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 244 | 39% helix, 26% strand | P21242 |
| G, U | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 243 | 40% helix, 23% strand | P21243 |
| H, V | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 222 | 29% helix, 35% strand | P25043 |
| I, W | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 30% helix, 32% strand | P25451 |
| J, X | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 198 | 34% helix, 32% strand | P22141 |
| K | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 212 | 36% helix, 33% strand | P30656 |
| L, Z | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 222 | 28% helix, 32% strand | P23724 |
| M, a | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 233 | 32% helix, 31% strand | P30657 |
| N, b | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 196 | 38% helix, 35% strand | P38624 |
| Y | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 211 | 36% helix, 34% strand | P30656 |
Ligands and binding sites
- 2YD · (5R,6R,7S,8R,9R,12S,13E,16S,18S,19R,20aR)-4,7,19-trihydroxy-2,6,8,12,14,16,18-heptamethyl-6,7,8,9,10,11,12,15,16,17,18,19,20,20a-tetradecahydro-1,19:5,9-diepoxybenzo[18]annulen-3(5H)-one · ligand · 2 copies · chains H, a, M, 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 | 1073 | 0.83 | 0.84 | 157 | empty |
| 2 | 758 | 0.81 | 0.85 | 102 | empty |
| 3 | 769 | 0.81 | 0.84 | 85 | empty |
| 4 | 1018 | 0.80 | 0.82 | 102 | empty |
| 5 | 1022 | 0.79 | 0.81 | 104 | empty |
Interfaces
92 interfaces between chains.
- V–W · 1755 Ų buried · 32 hydrogen bonds · protein-protein
- H–I · 1752 Ų buried · 29 hydrogen bonds · protein-protein
- P–Q · 1633 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1628 Ų buried · 25 hydrogen bonds · protein-protein
- L–V · 1494 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4Q1S · Yeast 20S proteasome in Complex with Kendomycin · the same entry in another collection · chain A against A, 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 P23639
- Every structure of UniProt P23638
- Every structure of UniProt P40303
- Every structure of UniProt P32379
- Every structure of UniProt P40302
- Every structure of UniProt P21242
- Every structure of UniProt P21243
- Every structure of UniProt P25043
- Every structure of UniProt P25451
- Every structure of UniProt P22141
- Every structure of UniProt P30656
- Every structure of UniProt P23724
- Every structure of UniProt P30657
- Every structure of UniProt P38624
- Elsewhere: RCSB PDB 4Q1S · PDBe 4Q1S · UniProt P23639 · UniProt P23638 · UniProt P40303 · UniProt P32379 · UniProt P40302 · UniProt P21242 · UniProt P21243 · UniProt P25043 · UniProt P25451 · UniProt P22141 · UniProt P30656 · UniProt P23724 · UniProt P30657 · UniProt P38624
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