Research workbench
Dengue virus protease covalently bound to a peptide
Analyse Dengue virus protease covalently bound to a peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U1I
- Type
- protein
- Length
- 415 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine protease subunit NS2B; Serine protease NS3; Peptide of (BEZ)(NLE)KR(OAR)
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13
- UniProt
- Q5UB51
- Ligands
- OAR, BEZ, SO4
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 5 distinct chains · 2% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Serine protease subunit NS2B | protein | 39 | 0% helix, 51% strand | Q5UB51 |
| B | Serine protease NS3 (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 168 | 2% helix, 43% strand | Q5UB51 |
| D | Serine protease NS3 (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 165 | 2% helix, 47% strand | Q5UB51 |
| E | Peptide of (BEZ)(NLE)KR(OAR) | protein | 1 | 0% helix, 0% strand | — |
| F | Peptide of (BEZ)(NLE)KR(OAR) | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- OAR · N-(4-amino-5-hydroxy-pentyl)-guanidine · ligand · 2 copies · chains C, D, E, B, F
- BEZ · Benzoic acid · ligand · chains B, F
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.55 | 0.80 | 24 | empty |
| 2 | 97 | 0.47 | 0.80 | 21 | empty |
| 3 | 60 | 0.27 | 0.73 | 15 | SO4 |
Interfaces
9 interfaces between chains.
- A–B · 2146 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2114 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 476 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 253 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 191 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 3U1I · Dengue virus protease covalently bound to a peptide · 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 Q5UB51
- Elsewhere: RCSB PDB 3U1I · PDBe 3U1I · UniProt Q5UB51
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