Research workbench
Structure of the mycobacterium tuberculosis 20S proteasome bound to the C-terminal gqyl motif of the ATP-bound mpa ATPase
Analyse Structure of the mycobacterium tuberculosis 20S proteasome bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8D6V
- Type
- protein
- Length
- 6,146 residues
- Chains
- 35
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit alpha; Proteasome subunit beta; Proteasome-associated ATPase
- EC
- 3.4.25.1
- UniProt
- A5U4D5, A0A045HFG5, A1KKF8
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 41% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G, H, I, J, K, L, M, N, O | Proteasome subunit alpha (EC 3.4.25.1) | protein | 215 | 41% helix, 25% strand | A5U4D5 |
| P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c | Proteasome subunit beta (EC 3.4.25.1) | protein | 222 | 41% helix, 30% strand | A0A045HFG5 |
| d, e, f, g, h, i, j | Proteasome-associated ATPase | protein | 4 | 0% helix, 0% strand | A1KKF8 |
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 | 618 | 0.84 | 0.88 | 46 | empty |
| 2 | 564 | 0.83 | 0.89 | 42 | empty |
| 3 | 575 | 0.83 | 0.89 | 47 | empty |
| 4 | 579 | 0.83 | 0.88 | 49 | empty |
| 5 | 573 | 0.83 | 0.88 | 48 | empty |
Interfaces
84 interfaces between chains.
- L–M · 819 Ų buried · 9 hydrogen bonds · protein-protein
- P–c · 784 Ų buried · 15 hydrogen bonds · protein-protein
- S–Z · 778 Ų buried · 14 hydrogen bonds · protein-protein
- M–N · 776 Ų buried · 7 hydrogen bonds · protein-protein
- V–W · 771 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 8D6V · Structure of the Mycobacterium tuberculosis 20S proteasome bound to the C-terminal GQYL… · 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 A5U4D5
- Every structure of UniProt A0A045HFG5
- Every structure of UniProt A1KKF8
- Elsewhere: RCSB PDB 8D6V · PDBe 8D6V · UniProt A5U4D5 · UniProt A0A045HFG5 · UniProt A1KKF8
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