Research workbench
Crystal structure of the 3C protease from south african territories type 2 foot-and-mouth disease virus
Analyse Crystal structure of the 3C protease from south african territories type 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HM2
- Type
- protein
- Length
- 1,005 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C proteinase
- UniProt
- Q1EF85
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | 3C proteinase | protein | 201 | 12% helix, 50% strand | Q1EF85 |
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.71 | 0.82 | 54 | empty |
| 2 | 453 | 0.69 | 0.80 | 54 | empty |
| 3 | 376 | 0.65 | 0.79 | 43 | empty |
| 4 | 315 | 0.64 | 0.80 | 25 | empty |
| 5 | 398 | 0.62 | 0.77 | 49 | empty |
Interfaces
7 interfaces between chains.
- B–C · 932 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 919 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 867 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 844 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 144 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5HM2 · Crystal structure of the 3C protease from South African Territories type 2 foot-and-mouth… · the same entry in another collection · chain A against A, 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 Q1EF85
- Elsewhere: RCSB PDB 5HM2 · PDBe 5HM2 · UniProt Q1EF85
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