Research workbench
Crystal structure of full length NS3 protein (ED4NS2BNS3) from DENV4 in closed conformation
Analyse Crystal structure of full length NS3 protein (ED4NS2BNS3) from DENV4 in closed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YVW
- Type
- protein
- Length
- 621 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- UniProt
- F8TEL4
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Genome polyprotein | protein | 591 | 25% helix, 20% strand | F8TEL4 |
| A | Genome polyprotein | protein | 30 | 0% helix, 27% strand | F8TEL4 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.81 | 0.82 | 87 | empty |
| 2 | 639 | 0.67 | 0.77 | 74 | EPE |
| 3 | 64 | 0.44 | 0.82 | 26 | empty |
| 4 | 73 | 0.43 | 0.81 | 16 | empty |
| 5 | 62 | 0.40 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 1237 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5YVW · Crystal structure of full length NS3 protein (eD4NS2BNS3) from DENV4 in closed… · the same entry in another collection · chain B against B, 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 F8TEL4
- Elsewhere: RCSB PDB 5YVW · PDBe 5YVW · UniProt F8TEL4
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