Research workbench
Crystal structure of streptococcus pneumoniae nana (TIGR4) in complex with dana
Analyse Crystal structure of streptococcus pneumoniae nana (TIGR4) in complex with dana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YA6
- Type
- protein
- Length
- 940 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase a
- EC
- 3.2.1.18
- UniProt
- B2DJD9
- Ligands
- DAN, CL
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuraminidase a (EC 3.2.1.18) | protein | 470 | 6% helix, 46% strand | B2DJD9 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- FMT · Formic acid · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.77 | 0.80 | 93 | FMT |
| 2 | 304 | 0.63 | 0.80 | 29 | empty |
| 3 | 291 | 0.61 | 0.79 | 26 | FMT |
| 4 | 83 | 0.58 | 0.87 | 30 | empty |
| 5 | 107 | 0.57 | 0.85 | 21 | DAN |
Interfaces
1 interface between chains.
- A–B · 1238 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2YA6 · Crystal structure of Streptococcus pneumoniae NanA (TIGR4) in complex with DANA · 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 2YA6 · PDBe 2YA6 · UniProt B2DJD9
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