Research workbench
Crystal structure of the NS1 effector domain from influenza A/VIETNAM/1203/2004 (H5N1) virus
Analyse Crystal structure of the NS1 effector domain from influenza A/VIETNAM/1203/2004… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P31
- Type
- protein
- Length
- 484 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nonstructural protein 1
- UniProt
- D1LP63
- Ligands
- SCN
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nonstructural protein 1 | protein | 120 | 23% helix, 38% strand | D1LP63 |
| B | Nonstructural protein 1 | protein | 121 | 24% helix, 40% strand | D1LP63 |
| C | Nonstructural protein 1 | protein | 122 | 22% helix, 41% strand | D1LP63 |
| D | Nonstructural protein 1 | protein | 121 | 22% helix, 41% strand | D1LP63 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 8 copies · chains A, B, C, D
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 | 950 | 0.72 | 0.76 | 53 | empty |
| 2 | 82 | 0.43 | 0.80 | 15 | empty |
| 3 | 89 | 0.41 | 0.78 | 15 | empty |
| 4 | 80 | 0.38 | 0.77 | 17 | empty |
| 5 | 52 | 0.37 | 0.80 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–D · 626 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 624 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 511 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 490 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 10 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3P31 · Crystal structure of the NS1 effector domain from influenza A/Vietnam/1203/2004 (H5N1)… · 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 D1LP63
- Elsewhere: RCSB PDB 3P31 · PDBe 3P31 · UniProt D1LP63
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