Research workbench
Yeast 20S proteasome in complex with blm-pep activator
Analyse Yeast 20S proteasome in complex with blm-pep activator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NIF
- Type
- protein
- Length
- 6,352 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit alpha type-1; Proteasome subunit alpha type-2; Proteasome subunit…
- EC
- 3.4.25.1
- UniProt
- P21243, P23639, P23638, P40303, P32379, P40302, P21242, P38624, P25043, P25451, P22141, P30656, P23724, P30657
- Ligands
- MG, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 18 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 241 | 41% helix, 22% strand | P21243 |
| B, P | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 250 | 36% helix, 25% strand | P23639 |
| C | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 241 | 35% helix, 26% strand | P23638 |
| D, R | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 241 | 34% helix, 25% strand | P40303 |
| E | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 236 | 38% helix, 28% strand | P32379 |
| F, T | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 232 | 37% helix, 28% strand | P40302 |
| G, U | Probable proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 244 | 38% helix, 27% strand | P21242 |
| H, V | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 196 | 37% helix, 34% strand | P38624 |
| I, W | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 222 | 29% helix, 34% strand | P25043 |
| J, X | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 32% helix, 30% strand | P25451 |
| K, Y | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 196 | 34% helix, 34% strand | P22141 |
| L, Z | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 212 | 36% helix, 34% strand | P30656 |
| M, 1 | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 222 | 29% helix, 31% strand | P23724 |
| N | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 232 | 32% helix, 31% strand | P30657 |
| Q | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 242 | 36% helix, 26% strand | P23638 |
| S | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 236 | 39% helix, 28% strand | P32379 |
| 2 | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 233 | 31% helix, 30% strand | P30657 |
| 3, 4 | TRP-arg-ser-tyr-tyr-ala | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains C, D, H, I, J, N, Q
- CL · Chloride ion · ion · 12 copies · chains A, G, K, F, N, O, P, R, S, T, V, W, 2
- EDO · 1,2-ethanediol · additive · 16 copies · chains C, F, N, G, H, I, L, M, O, P, W, U, V, Y, R, 1, 2
- GOL · Glycerol · additive · 7 copies · chains J, K, L, M, N, Q, X, V, Z, 1
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 | 818 | 0.81 | 0.84 | 113 | empty |
| 2 | 776 | 0.80 | 0.84 | 95 | empty |
| 3 | 1046 | 0.80 | 0.81 | 120 | GOL |
| 4 | 937 | 0.79 | 0.81 | 99 | empty |
| 5 | 1005 | 0.79 | 0.81 | 126 | empty |
Interfaces
94 interfaces between chains.
- W–X · 1682 Ų buried · 27 hydrogen bonds · protein-protein
- I–J · 1654 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1548 Ų buried · 25 hydrogen bonds · protein-protein
- Q–R · 1526 Ų buried · 21 hydrogen bonds · protein-protein
- M–W · 1480 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5NIF · Yeast 20S proteasome in complex with Blm-pep activator · 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 P21243
- 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 P38624
- 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
- Elsewhere: RCSB PDB 5NIF · PDBe 5NIF · UniProt P21243 · UniProt P23639 · UniProt P23638 · UniProt P40303 · UniProt P32379 · UniProt P40302 · UniProt P21242 · UniProt P38624 · UniProt P25043 · UniProt P25451 · UniProt P22141 · UniProt P30656 · UniProt P23724 · UniProt P30657
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