Research workbench
Crystal structure of streptococcus pneumoniae nana (TIGR4) in complex with sialic acid
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
- 2YA5
- Type
- protein
- Length
- 941 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
- SIA, CL
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuraminidase a (EC 3.2.1.18) | protein | 471 | 6% helix, 46% strand | B2DJD9 |
| B | Neuraminidase a (EC 3.2.1.18) | protein | 470 | 6% helix, 45% strand | B2DJD9 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 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
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.77 | 0.80 | 102 | FMT |
| 2 | 313 | 0.63 | 0.80 | 35 | empty |
| 3 | 297 | 0.61 | 0.79 | 23 | FMT |
| 4 | 268 | 0.56 | 0.77 | 38 | empty |
| 5 | 263 | 0.55 | 0.76 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1204 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2YA5 · Crystal structure of Streptococcus pneumoniae NanA (TIGR4) in complex with sialic acid · 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 B2DJD9
- Elsewhere: RCSB PDB 2YA5 · PDBe 2YA5 · UniProt B2DJD9
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