Research workbench
Yeast 20S proteasome in complex with pr-VI modulator
Analyse Yeast 20S proteasome in complex with pr-VI modulator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X6Z
- Type
- protein
- Length
- 6,359 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit beta type-6; Proteasome subunit beta type-7; Proteasome subunit alpha…
- EC
- 3.4.25.1
- UniProt
- P23724, P30657, P21243, P23639, P23638, P40303, P32379, P40302, P21242, P38624, P25043, P25451, P22141, P30656
- Ligands
- MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 18 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, M | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 222 | 29% helix, 32% strand | P23724 |
| 2, N | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 233 | 31% helix, 30% strand | P30657 |
| A | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 242 | 40% helix, 23% strand | P21243 |
| B | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 248 | 35% helix, 26% strand | P23639 |
| C, Q | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 244 | 35% helix, 25% strand | P23638 |
| D, R | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 241 | 36% helix, 24% strand | P40303 |
| E, S | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 242 | 36% helix, 26% strand | P32379 |
| F, T | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 232 | 34% helix, 28% strand | P40302 |
| G, U | Probable proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 244 | 39% helix, 26% strand | P21242 |
| H, V | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 196 | 38% helix, 35% strand | P38624 |
| I | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 221 | 29% helix, 34% strand | P25043 |
| J, X | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 32% helix, 33% 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 |
| O | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 241 | 39% helix, 23% strand | P21243 |
| P | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 249 | 35% helix, 26% strand | P23639 |
| W | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 220 | 30% helix, 35% strand | P25043 |
| a, e | Synthetic peptide (polymer) | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 56 copies · chains 1, 2, T, I, B, C, D, F, H, J, K, L, E, M, N, G, O, P, Q, R, S, V, W, U, X, Y, Z
- GOL · Glycerol · additive · 38 copies · chains 1, Z, 2, V, A, H, I, G, D, E, F, N, B, J, K, L, Y, M, O, W, U, S, T, X
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 9 copies · chains 1, 2, K, L, M, N, T, V, P, W, X, Z
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 | 970 | 0.83 | 0.84 | 151 | MPD |
| 2 | 979 | 0.80 | 0.81 | 109 | empty |
| 3 | 1012 | 0.79 | 0.81 | 112 | MG |
| 4 | 981 | 0.79 | 0.81 | 97 | MG |
| 5 | 1025 | 0.79 | 0.81 | 102 | MG |
Interfaces
95 interfaces between chains.
- I–J · 1760 Ų buried · 27 hydrogen bonds · protein-protein
- W–X · 1687 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1651 Ų buried · 26 hydrogen bonds · protein-protein
- Q–R · 1641 Ų buried · 26 hydrogen bonds · protein-protein
- 1–I · 1513 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4X6Z · Yeast 20S proteasome in complex with PR-VI modulator · the same entry in another collection · chain 2 against 2, 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 P23724
- Every structure of UniProt P30657
- 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
- Elsewhere: RCSB PDB 4X6Z · PDBe 4X6Z · UniProt P23724 · UniProt P30657 · UniProt P21243 · UniProt P23639 · UniProt P23638 · UniProt P40303 · UniProt P32379 · UniProt P40302 · UniProt P21242 · UniProt P38624 · UniProt P25043 · UniProt P25451 · UniProt P22141 · UniProt P30656
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