Research workbench
The structure of the Plasmodium falciparum 20S proteasome in complex with two PA28 activators
Analyse The structure of the Plasmodium falciparum 20S proteasome in complex with two… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MUV
- Type
- protein
- Length
- 8,796 residues
- Chains
- 42
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.8
- Source
- Plasmodium falciparum (isolate 3D7)
- Molecule
- 20S proteasome alpha-1 subunit; 20S proteasome alpha-2 subunit; 20S proteasome alpha-3…
- EC
- 3.4.25.1
- UniProt
- Q8IAR3, C6KST3, Q8IDG3, Q8IDG2, Q8IBI3, Q8IK90, O77396, Q8I0U7, Q8I6T3, Q8I261, Q8IKC9, Q8IJT1, C0H4E8, Q7K6A9, Q8I374
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · resolution 3.8 · 19 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | 20S proteasome alpha-1 subunit (EC 3.4.25.1) | protein | 246 | 36% helix, 17% strand | Q8IAR3 |
| B, P | 20S proteasome alpha-2 subunit (EC 3.4.25.1) | protein | 224 | 33% helix, 21% strand | C6KST3 |
| C, Q | 20S proteasome alpha-3 subunit (EC 3.4.25.1) | protein | 240 | 34% helix, 15% strand | Q8IDG3 |
| D, R | 20S proteasome alpha-4 subunit (EC 3.4.25.1) | protein | 227 | 34% helix, 18% strand | Q8IDG2 |
| E, S | 20S proteasome alpha-5 subunit (EC 3.4.25.1) | protein | 227 | 31% helix, 17% strand | Q8IBI3 |
| F, T | 20S proteasome alpha-6 subunit (EC 3.4.25.1) | protein | 236 | 33% helix, 19% strand | Q8IK90 |
| G, U | 20S proteasome alpha-7 subunit (EC 3.4.25.1) | protein | 233 | 29% helix, 20% strand | O77396 |
| H, V | 20S proteasome beta-1 subunit (EC 3.4.25.1) | protein | 193 | 29% helix, 22% strand | Q8I0U7 |
| I, W | 20S proteasome beta-2 subunit (EC 3.4.25.1) | protein | 219 | 27% helix, 23% strand | Q8I6T3 |
| J, X | 20S proteasome beta-3 subunit (EC 3.4.25.1) | protein | 203 | 26% helix, 23% strand | Q8I261 |
| K, Y | 20S proteasome beta-4 subunit (EC 3.4.25.1) | protein | 195 | 31% helix, 26% strand | Q8IKC9 |
| L, Z | 20S proteasome beta-5 subunit (EC 3.4.25.1) | protein | 204 | 29% helix, 17% strand | Q8IJT1 |
| M, a | 20S proteasome beta-6 subunit (EC 3.4.25.1) | protein | 211 | 29% helix, 26% strand | C0H4E8 |
| N, b | 20S proteasome beta-7 subunit (EC 3.4.25.1) | protein | 224 | 30% helix, 19% strand | Q7K6A9 |
| c, d, m, o | Proteasome activator PA28 | protein | 187 | 80% helix, 0% strand | Q8I374 |
| e, p | Proteasome activator PA28 | protein | 188 | 79% helix, 0% strand | Q8I374 |
| f, j | Proteasome activator PA28 | protein | 193 | 77% helix, 0% strand | Q8I374 |
| g, k | Proteasome activator PA28 | protein | 189 | 78% helix, 0% strand | Q8I374 |
| h, i, l, n | Proteasome activator PA28 | protein | 186 | 80% helix, 0% strand | Q8I374 |
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 | 1133 | 0.81 | 0.82 | 116 | empty |
| 2 | 811 | 0.80 | 0.83 | 89 | empty |
| 3 | 625 | 0.78 | 0.83 | 90 | empty |
| 4 | 725 | 0.78 | 0.82 | 72 | empty |
| 5 | 952 | 0.78 | 0.80 | 96 | empty |
Interfaces
116 interfaces between chains.
- g–h · 2125 Ų buried · 20 hydrogen bonds · protein-protein
- j–p · 2117 Ų buried · 15 hydrogen bonds · protein-protein
- k–l · 2110 Ų buried · 16 hydrogen bonds · protein-protein
- e–f · 2107 Ų buried · 17 hydrogen bonds · protein-protein
- c–i · 2102 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6MUV · The structure of the plasmodium falciparum 20S proteasome in complex with two PA28… · 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 Q8IAR3
- Every structure of UniProt C6KST3
- Every structure of UniProt Q8IDG3
- Every structure of UniProt Q8IDG2
- Every structure of UniProt Q8IBI3
- Every structure of UniProt Q8IK90
- Every structure of UniProt O77396
- Every structure of UniProt Q8I0U7
- Every structure of UniProt Q8I6T3
- Every structure of UniProt Q8I261
- Every structure of UniProt Q8IKC9
- Every structure of UniProt Q8IJT1
- Every structure of UniProt C0H4E8
- Every structure of UniProt Q7K6A9
- Every structure of UniProt Q8I374
- Elsewhere: RCSB PDB 6MUV · PDBe 6MUV · UniProt Q8IAR3 · UniProt C6KST3 · UniProt Q8IDG3 · UniProt Q8IDG2 · UniProt Q8IBI3 · UniProt Q8IK90 · UniProt O77396 · UniProt Q8I0U7 · UniProt Q8I6T3 · UniProt Q8I261 · UniProt Q8IKC9 · UniProt Q8IJT1 · UniProt C0H4E8 · UniProt Q7K6A9 · UniProt Q8I374
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