MolNFT v1 · #81326 · protein
Mouse constitutive 20S proteasome in complex with pr-957
3UNB · Proteasome subunit alpha type-2: “Mouse constitutive 20S proteasome in complex with pr-957”. X-ray diffraction, 1 ligand (04C), 20 pockets (best druggability 0.81). MolNFT v1 #81326 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3UNB
- Type
- protein
- Length
- 12,512 residues
- Chains
- 56
- 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
- P49722, Q9R1P0, Q9Z2U0, Q9Z2U1, Q9R1P4, O70435, Q9QUM9, P70195, Q9R1P1, Q9R1P3, O55234, O09061, P99026, Q60692
- Ligands
- 04C
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 14 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O, c, q | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 231 | 35% helix, 26% strand | P49722 |
| B, P, d, r | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 248 | 38% helix, 26% strand | Q9R1P0 |
| C, Q, e, s | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 239 | 35% helix, 24% strand | Q9Z2U0 |
| D, R, f, t | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 233 | 33% helix, 26% strand | Q9Z2U1 |
| E, S, g, u | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 238 | 31% helix, 25% strand | Q9R1P4 |
| F, T, h, v | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 244 | 34% helix, 25% strand | O70435 |
| G, U, i, w | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 243 | 38% helix, 25% strand | Q9QUM9 |
| H, V, j, x | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 220 | 30% helix, 33% strand | P70195 |
| I, W, k, y | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 30% helix, 31% strand | Q9R1P1 |
| J, X, l, z | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 196 | 32% helix, 33% strand | Q9R1P3 |
| K, Y, m, 1 | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 201 | 35% helix, 33% strand | O55234 |
| L, Z, n, 2 | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 213 | 31% helix, 31% strand | O09061 |
| M, a, o, 3 | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 216 | 34% helix, 34% strand | P99026 |
| N, b, p, 4 | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 202 | 35% helix, 32% strand | Q60692 |
Ligands and binding sites
- 04C · 1,2,4-trideoxy-4-methyl-2-{[N-(morpholin-4-ylacetyl)-L-alanyl-O-methyl-L-tyrosyl]amino}-1-phenyl-D-xylitol · ligand · 12 copies · chains H, I, K, L, N, V, W, Y, Z, b, j, k, m, n, p, x, y, 1, 2, 4
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 | 967 | 0.81 | 0.82 | 114 | empty |
| 2 | 857 | 0.81 | 0.83 | 84 | empty |
| 3 | 924 | 0.81 | 0.82 | 110 | empty |
| 4 | 823 | 0.80 | 0.83 | 86 | empty |
| 5 | 1009 | 0.80 | 0.81 | 89 | empty |
Interfaces
177 interfaces between chains.
- x–y · 1748 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 1747 Ų buried · 31 hydrogen bonds · protein-protein
- V–W · 1744 Ų buried · 28 hydrogen bonds · protein-protein
- j–k · 1730 Ų buried · 27 hydrogen bonds · protein-protein
- d–e · 1596 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent, 8 disulfide (covalent ligand, disulfide).
Compared structures
- 3UNB · Mouse constitutive 20S proteasome in complex with PR-957 · 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 P49722
- Every structure of UniProt Q9R1P0
- Every structure of UniProt Q9Z2U0
- Every structure of UniProt Q9Z2U1
- Every structure of UniProt Q9R1P4
- Every structure of UniProt O70435
- Every structure of UniProt Q9QUM9
- Every structure of UniProt P70195
- Every structure of UniProt Q9R1P1
- Every structure of UniProt Q9R1P3
- Every structure of UniProt O55234
- Every structure of UniProt O09061
- Every structure of UniProt P99026
- Every structure of UniProt Q60692
- Elsewhere: RCSB PDB 3UNB · PDBe 3UNB · UniProt P49722 · UniProt Q9R1P0 · UniProt Q9Z2U0 · UniProt Q9Z2U1 · UniProt Q9R1P4 · UniProt O70435 · UniProt Q9QUM9 · UniProt P70195 · UniProt Q9R1P1 · UniProt Q9R1P3 · UniProt O55234 · UniProt O09061 · UniProt P99026 · UniProt Q60692
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