Research workbench
Structure of the foot-and-mouth disease virus leader proteinase in complex with inhibitor (N~2~-[(3S)-4-({(2R)-1-[(4- CARBAMIMIDAMIDOBUTYL)AMINO]-4-methyl-1-oxopentan-2-YL}AMINO)-3- hydroxy-4-oxobutanoyl]-L-arginyl-L-prolinamide)
Analyse Structure of the foot-and-mouth disease virus leader proteinase 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
- 4QBB
- Type
- protein
- Length
- 472 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leader protease
- EC
- 3.4.22.46
- UniProt
- P03305
- Ligands
- E69, K, PO4
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leader protease (EC 3.4.22.46) | protein | 159 | 28% helix, 24% strand | P03305 |
| B | Leader protease (EC 3.4.22.46) | protein | 156 | 29% helix, 24% strand | P03305 |
| C | Leader protease (EC 3.4.22.46) | protein | 157 | 29% helix, 27% strand | P03305 |
Ligands and binding sites
- E69 · N~2~-[(3S)-4-({(2R)-1-[(4-carbamimidamidobutyl)amino]-4-methyl-1-oxopentan-2-yl}amino)-3-hydroxy-4-oxobutanoyl]-L-arginyl-L-prolinamide · ligand · 3 copies · chains A, B, C
- K · Potassium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.55 | 0.77 | 33 | empty |
| 2 | 130 | 0.50 | 0.79 | 26 | empty |
| 3 | 125 | 0.36 | 0.73 | 22 | empty |
| 4 | 61 | 0.30 | 0.75 | 14 | empty |
| 5 | 51 | 0.28 | 0.75 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 505 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 85 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4QBB · Structure of the foot-and-mouth disease virus leader proteinase in complex with inhibitor… · 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 P03305
- Elsewhere: RCSB PDB 4QBB · PDBe 4QBB · UniProt P03305
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.