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Crystal structure of mycobacterium tuberculosis proteasome modified by inhibitor GL1
Analyse Crystal structure of mycobacterium tuberculosis proteasome modified by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H6I
- Type
- protein
- Length
- 6,043 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome (alpha subunit) prca; Proteasome (beta subunit) prcb
- EC
- 3.4.25.1
- UniProt
- O33244, O33245
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 15 distinct chains · 42% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteasome (alpha subunit) prca (EC 3.4.25.1) | protein | 216 | 44% helix, 26% strand | O33244 |
| B | Proteasome (alpha subunit) prca (EC 3.4.25.1) | protein | 214 | 41% helix, 25% strand | O33244 |
| C, Z, 2 | Proteasome (beta subunit) prcb (EC 3.4.25.1) | protein | 215 | 41% helix, 29% strand | O33245 |
| D, Y | Proteasome (alpha subunit) prca (EC 3.4.25.1) | protein | 213 | 41% helix, 24% strand | O33244 |
| E, G, J, L, P, T, X | Proteasome (beta subunit) prcb (EC 3.4.25.1) | protein | 216 | 39% helix, 29% strand | O33245 |
| F | Proteasome (alpha subunit) prca (EC 3.4.25.1) | protein | 217 | 43% helix, 24% strand | O33244 |
| H | Proteasome (beta subunit) prcb (EC 3.4.25.1) | protein | 213 | 41% helix, 30% strand | O33245 |
| I, 1 | Proteasome (alpha subunit) prca (EC 3.4.25.1) | protein | 215 | 43% helix, 25% strand | O33244 |
| K, W | Proteasome (alpha subunit) prca (EC 3.4.25.1) | protein | 217 | 41% helix, 24% strand | O33244 |
| M | Proteasome (alpha subunit) prca (EC 3.4.25.1) | protein | 216 | 41% helix, 25% strand | O33244 |
| N | Proteasome (beta subunit) prcb (EC 3.4.25.1) | protein | 213 | 40% helix, 30% strand | O33245 |
| O, S, U | Proteasome (alpha subunit) prca (EC 3.4.25.1) | protein | 215 | 44% helix, 25% strand | O33244 |
| Q | Proteasome (alpha subunit) prca (EC 3.4.25.1) | protein | 218 | 43% helix, 24% strand | O33244 |
| R | Proteasome (beta subunit) prcb (EC 3.4.25.1) | protein | 223 | 42% helix, 27% strand | O33245 |
| V | Proteasome (beta subunit) prcb (EC 3.4.25.1) | protein | 221 | 42% helix, 29% strand | O33245 |
Ligands and binding sites
- DMF · Dimethylformamide · additive · 102 copies · chains A, H, B, C, J, E, R, I, D, K, L, F, G, W, 2, X, P, N, M, V, O, Q, Z, S, T, 1, U, Y
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 | 926 | 0.85 | 0.87 | 86 | DMF |
| 2 | 1054 | 0.85 | 0.86 | 96 | DMF |
| 3 | 571 | 0.84 | 0.89 | 45 | DMF |
| 4 | 552 | 0.84 | 0.90 | 44 | DMF |
| 5 | 576 | 0.83 | 0.89 | 47 | DMF |
Interfaces
70 interfaces between chains.
- K–M · 975 Ų buried · 17 hydrogen bonds · protein-protein
- O–U · 952 Ų buried · 12 hydrogen bonds · protein-protein
- Q–Y · 950 Ų buried · 16 hydrogen bonds · protein-protein
- D–Q · 936 Ų buried · 13 hydrogen bonds · protein-protein
- F–W · 935 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (nonstandard).
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 O33244
- Every structure of UniProt O33245
- Elsewhere: RCSB PDB 3H6I · PDBe 3H6I · UniProt O33244 · UniProt O33245
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