MolNFT v1 · #81330 · protein
Mouse 20S immunoproteasome in complex with pr-957
3UNF · Proteasome subunit alpha type-2: “Mouse 20S immunoproteasome in complex with pr-957”. X-ray diffraction, 4 ligands (04C, K, CL), 20 pockets (best druggability 0.80). MolNFT v1 #81330 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3UNF
- Type
- protein
- Length
- 6,244 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-4; Proteasome subunit…
- UniProt
- P49722, Q9R1P0, Q9Z2U0, Q9Z2U1, Q9R1P4, O70435, Q9QUM9, P70195, Q9R1P1, Q9R1P3, O55234, O09061, P99026, Q60692
- Ligands
- 04C, K, CL, IOD
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 14 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | Proteasome subunit alpha type-2 | protein | 230 | 34% helix, 26% strand | P49722 |
| B, P | Proteasome subunit alpha type-4 | protein | 248 | 36% helix, 26% strand | Q9R1P0 |
| C, Q | Proteasome subunit alpha type-7 | protein | 238 | 37% helix, 24% strand | Q9Z2U0 |
| D, R | Proteasome subunit alpha type-5 | protein | 233 | 32% helix, 27% strand | Q9Z2U1 |
| E, S | Proteasome subunit alpha type-1 | protein | 238 | 35% helix, 25% strand | Q9R1P4 |
| F, T | Proteasome subunit alpha type-3 | protein | 244 | 34% helix, 26% strand | O70435 |
| G, U | Proteasome subunit alpha type-6 | protein | 243 | 39% helix, 24% strand | Q9QUM9 |
| H, V | Proteasome subunit beta type-10 | protein | 219 | 30% helix, 36% strand | P70195 |
| I, W | Proteasome subunit beta type-3 | protein | 204 | 31% helix, 33% strand | Q9R1P1 |
| J, X | Proteasome subunit beta type-2 | protein | 196 | 33% helix, 36% strand | Q9R1P3 |
| K, Y | Proteasome subunit beta type-8 | protein | 201 | 35% helix, 34% strand | O55234 |
| L, Z | Proteasome subunit beta type-1 | protein | 213 | 30% helix, 31% strand | O09061 |
| M, a | Proteasome subunit beta type-4 | protein | 216 | 35% helix, 33% strand | P99026 |
| N, b | Proteasome subunit beta type-9 | protein | 199 | 36% helix, 30% 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 · 6 copies · chains H, I, K, L, N, V, W, Y, Z, b
- K · Potassium ion · metal · 13 copies · chains B, A, G, I, J, K, L, V, M, P, R, S, Z, Y, a, b
- CL · Chloride ion · ion · 41 copies · chains A, C, D, E, H, I, J, L, K, M, V, b, N, O, P, Q, R, S, U, W, X, Z, a
- IOD · Iodide ion · ion · 6 copies · chains H, K, N, V, Y, b
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 | 764 | 0.80 | 0.84 | 74 | empty |
| 2 | 787 | 0.80 | 0.83 | 73 | CL |
| 3 | 1177 | 0.80 | 0.82 | 153 | 04C, CL, IOD |
| 4 | 885 | 0.79 | 0.81 | 116 | 04C, IOD, K |
| 5 | 980 | 0.78 | 0.80 | 99 | CL |
Interfaces
90 interfaces between chains.
- H–I · 1605 Ų buried · 25 hydrogen bonds · protein-protein
- V–W · 1602 Ų buried · 25 hydrogen bonds · protein-protein
- O–P · 1545 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1536 Ų buried · 16 hydrogen bonds · protein-protein
- P–Q · 1494 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 4 disulfide (covalent ligand, disulfide).
Compared structures
- 3UNF · Mouse 20S immunoproteasome in complex with PR-957 · 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 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 3UNF · PDBe 3UNF · 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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