Research workbench
Crystal structure of streptococcus pneumoniae nana (TIGR4) in complex with zanamivir
Analyse Crystal structure of streptococcus pneumoniae nana (TIGR4) 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
- 2YA7
- Type
- protein
- Length
- 1,877 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase a
- EC
- 3.2.1.18
- UniProt
- B2DJD9
- Ligands
- ZMR, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuraminidase a (EC 3.2.1.18) | protein | 469 | 6% helix, 45% strand | B2DJD9 |
| B | Neuraminidase a (EC 3.2.1.18) | protein | 468 | 4% helix, 45% strand | B2DJD9 |
| C, D | Neuraminidase a (EC 3.2.1.18) | protein | 470 | 6% helix, 46% strand | B2DJD9 |
Ligands and binding sites
- ZMR · Zanamivir · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.78 | 0.82 | 94 | empty |
| 2 | 620 | 0.75 | 0.82 | 76 | empty |
| 3 | 475 | 0.70 | 0.80 | 71 | empty |
| 4 | 326 | 0.68 | 0.82 | 52 | empty |
| 5 | 274 | 0.62 | 0.80 | 34 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1227 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1196 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 303 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 164 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 146 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2YA7 · Crystal structure of Streptococcus pneumoniae NanA (TIGR4) in complex with Zanamivir · 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 B2DJD9
- Elsewhere: RCSB PDB 2YA7 · PDBe 2YA7 · UniProt B2DJD9
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