MolNFT v1 · #159060 · protein
Crystal structure of mycobacterium tuberculosis proteasome in complex with phenylimidazole-based inhibitor A86
6OCZ · Proteasome subunit alpha: “Crystal structure of mycobacterium tuberculosis proteasome in complex with phenylimidazole-based inhibitor A86”. X-ray diffraction, 1 ligand (M6Y), 20 pockets (best druggability 0.86). MolNFT v1 #159060 on…
- PDB
- 6OCZ
- Type
- protein
- Length
- 6,147 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit alpha; Proteasome subunit beta
- EC
- 3.4.25.1
- UniProt
- P9WHU1, P9WHT9
- Ligands
- M6Y
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 16 distinct chains · 42% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteasome subunit alpha (EC 3.4.25.1) | protein | 218 | 42% helix, 26% strand | P9WHU1 |
| B | Proteasome subunit alpha (EC 3.4.25.1) | protein | 215 | 42% helix, 26% strand | P9WHU1 |
| C | Proteasome subunit alpha (EC 3.4.25.1) | protein | 217 | 44% helix, 26% strand | P9WHU1 |
| D | Proteasome subunit alpha (EC 3.4.25.1) | protein | 215 | 42% helix, 26% strand | P9WHU1 |
| E | Proteasome subunit alpha (EC 3.4.25.1) | protein | 217 | 43% helix, 26% strand | P9WHU1 |
| F | Proteasome subunit alpha (EC 3.4.25.1) | protein | 216 | 41% helix, 25% strand | P9WHU1 |
| G | Proteasome subunit alpha (EC 3.4.25.1) | protein | 215 | 41% helix, 26% strand | P9WHU1 |
| H, I, J, M, X, Z | Proteasome subunit beta (EC 3.4.25.1) | protein | 222 | 40% helix, 29% strand | P9WHT9 |
| K, L, N, V, W, Y, a, b | Proteasome subunit beta (EC 3.4.25.1) | protein | 223 | 40% helix, 29% strand | P9WHT9 |
| O | Proteasome subunit alpha (EC 3.4.25.1) | protein | 217 | 41% helix, 25% strand | P9WHU1 |
| P | Proteasome subunit alpha (EC 3.4.25.1) | protein | 219 | 41% helix, 25% strand | P9WHU1 |
| Q | Proteasome subunit alpha (EC 3.4.25.1) | protein | 216 | 43% helix, 26% strand | P9WHU1 |
| R | Proteasome subunit alpha (EC 3.4.25.1) | protein | 215 | 42% helix, 26% strand | P9WHU1 |
| S | Proteasome subunit alpha (EC 3.4.25.1) | protein | 218 | 43% helix, 25% strand | P9WHU1 |
| T | Proteasome subunit alpha (EC 3.4.25.1) | protein | 217 | 43% helix, 26% strand | P9WHU1 |
| U | Proteasome subunit alpha (EC 3.4.25.1) | protein | 216 | 41% helix, 25% strand | P9WHU1 |
Ligands and binding sites
- M6Y · N-{(2S)-1-({(2S)-1-[(2,4-difluorobenzyl)amino]-1-oxopropan-2-yl}amino)-1,4-dioxo-4-[(2R)-2-phenylpyrrolidin-1-yl]butan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide (non-preferred name) · ligand · 14 copies · chains H, I, J, K, L, M, N, V, W, X, Y, Z, a, b
- DMF · Dimethylformamide · additive · 20 copies · chains A, B, C, E, F, N, G, H, I, J, O, P, Q, R, Y, S, T, U
- CIT · Citric acid · additive · 14 copies · chains H, Y, I, X, J, W, K, V, L, b, M, a, N, 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 | 1054 | 0.86 | 0.87 | 97 | M6Y |
| 2 | 1096 | 0.86 | 0.87 | 105 | M6Y |
| 3 | 1123 | 0.85 | 0.86 | 98 | M6Y, CIT |
| 4 | 580 | 0.84 | 0.90 | 46 | empty |
| 5 | 551 | 0.84 | 0.89 | 48 | empty |
Interfaces
70 interfaces between chains.
- A–G · 953 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 923 Ų buried · 16 hydrogen bonds · protein-protein
- S–T · 896 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 895 Ų buried · 13 hydrogen bonds · protein-protein
- O–U · 893 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- P9WHT9 · AlphaFold monomer V2.0 prediction for proteasome subunit beta (P9WHT9) · a predicted model of the same protein · chain K against A, TM-score 1.00
- P9WHU1 · AlphaFold monomer V2.0 prediction for proteasome subunit alpha (P9WHU1) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 P9WHU1
- Every structure of UniProt P9WHT9
- Elsewhere: RCSB PDB 6OCZ · PDBe 6OCZ · UniProt P9WHU1 · UniProt P9WHT9
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