Research workbench
Crystal structure of mycobacterium tuberculosis proteasome in complex with N,C-capped dipeptide inhibitor PKS2205
Analyse Crystal structure of mycobacterium tuberculosis proteasome in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5THO
- Type
- protein
- Length
- 6,157 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
- A5U4D5, A5U4D6
- Ligands
- 7C7
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 11 distinct chains · 42% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G, O | Proteasome subunit alpha (EC 3.4.25.1) | protein | 218 | 41% helix, 26% strand | A5U4D5 |
| B | Proteasome subunit alpha (EC 3.4.25.1) | protein | 215 | 43% helix, 26% strand | A5U4D5 |
| C | Proteasome subunit alpha (EC 3.4.25.1) | protein | 217 | 42% helix, 26% strand | A5U4D5 |
| D | Proteasome subunit alpha (EC 3.4.25.1) | protein | 216 | 41% helix, 26% strand | A5U4D5 |
| F, R | Proteasome subunit alpha (EC 3.4.25.1) | protein | 217 | 42% helix, 25% strand | A5U4D5 |
| H, I, J, N, X, Z | Proteasome subunit beta (EC 3.4.25.1) | protein | 222 | 40% helix, 29% strand | A5U4D6 |
| K, L, M, V, W, Y, a, b | Proteasome subunit beta (EC 3.4.25.1) | protein | 223 | 40% helix, 29% strand | A5U4D6 |
| P, T | Proteasome subunit alpha (EC 3.4.25.1) | protein | 217 | 43% helix, 25% strand | A5U4D5 |
| Q | Proteasome subunit alpha (EC 3.4.25.1) | protein | 216 | 43% helix, 26% strand | A5U4D5 |
| S | Proteasome subunit alpha (EC 3.4.25.1) | protein | 221 | 42% helix, 25% strand | A5U4D5 |
| U | Proteasome subunit alpha (EC 3.4.25.1) | protein | 216 | 43% helix, 25% strand | A5U4D5 |
Ligands and binding sites
- 7C7 · N,N-diethyl-N~2~-(3-phenylpropanoyl)-L-asparaginyl-O-methyl-N-[(naphthalen-1-yl)methyl]-L-serinamide · ligand · 14 copies · chains H, I, J, K, L, M, N, V, W, X, Y, Z, a, b
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 | 558 | 0.84 | 0.90 | 50 | empty |
| 2 | 574 | 0.83 | 0.89 | 47 | empty |
| 3 | 574 | 0.83 | 0.88 | 42 | empty |
| 4 | 604 | 0.83 | 0.88 | 49 | empty |
| 5 | 580 | 0.83 | 0.88 | 44 | empty |
Interfaces
70 interfaces between chains.
- A–G · 921 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 918 Ų buried · 18 hydrogen bonds · protein-protein
- O–U · 915 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 884 Ų buried · 10 hydrogen bonds · protein-protein
- P–Q · 883 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5THO · Crystal Structure of Mycobacterium Tuberculosis Proteasome in complex with N,C-capped… · the same entry in another collection · chain I against I, 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 A5U4D6
- Elsewhere: RCSB PDB 5THO · PDBe 5THO · UniProt A5U4D5 · UniProt A5U4D6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.