MolNFT v1 · #36819 · protein
Crystal structure of mycobacterium tuberculosis proteasome in complex with a peptidyl boronate inhibitor mln-273
2FHH · 20S proteasome, alpha and beta subunits: “Crystal structure of mycobacterium tuberculosis proteasome in complex with a peptidyl boronate inhibitor…”. X-ray diffraction, 1 ligand (M1N), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 2FHH
- Type
- protein
- Length
- 6,188 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 20S proteasome, alpha and beta subunits; Proteasome, beta subunit
- Ligands
- M1N
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F, I, K, M, O, Q, S, U, W, Y, 1 | 20S proteasome, alpha and beta subunits | protein | 220 | 40% helix, 23% strand | — |
| H, C, E, G, J, L, N, P, R, T, V, X, Z, 2 | Proteasome, beta subunit | protein | 222 | 37% helix, 28% strand | — |
Ligands and binding sites
- M1N · (1R)-3-methyl-1-{[N-(morpholin-4-ylcarbonyl)-3-(1-naphthyl)-D-alanyl]amino}butylboronic acid · ligand · 14 copies · chains H, P, C, E, R, G, N, V, J, L, Z, T, 2, X
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 | 1119 | 0.84 | 0.85 | 98 | M1N |
| 2 | 568 | 0.84 | 0.89 | 47 | empty |
| 3 | 564 | 0.83 | 0.89 | 47 | empty |
| 4 | 544 | 0.83 | 0.89 | 43 | empty |
| 5 | 572 | 0.83 | 0.89 | 44 | empty |
Interfaces
70 interfaces between chains.
- B–I · 897 Ų buried · 8 hydrogen bonds · protein-protein
- F–W · 897 Ų buried · 13 hydrogen bonds · protein-protein
- F–M · 896 Ų buried · 11 hydrogen bonds · protein-protein
- Q–Y · 895 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 893 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 covalent (covalent ligand).
Compared structures
- 2FHH · Crystal Structure of Mycobacterium Tuberculosis Proteasome in complex with a peptidyl… · the same entry in another collection · chain N against N, 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
- Elsewhere: RCSB PDB 2FHH · PDBe 2FHH
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