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Crystal structure of streptococcus pneumoniae nanc, in complex with 3- sialyllactose
Analyse Crystal structure of streptococcus pneumoniae nanc, in complex with 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YZ5
- Type
- protein
- Length
- 1,310 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative neuraminidase
- EC
- 3.2.1.18
- UniProt
- Q97Q99
- Ligands
- DAN, GAL, SIA, SO4, GLC
- Pockets
- 16 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative neuraminidase (EC 3.2.1.18) | protein | 656 | 3% helix, 45% strand | Q97Q99 |
| B | Putative neuraminidase (EC 3.2.1.18) | protein | 654 | 4% helix, 45% strand | Q97Q99 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- GLC · alpha-D-glucopyranose · ion · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.70 | 0.97 | 23 | empty |
| 2 | 61 | 0.68 | 0.96 | 19 | empty |
| 3 | 254 | 0.66 | 0.83 | 41 | DAN |
| 4 | 265 | 0.66 | 0.83 | 45 | DAN |
| 5 | 356 | 0.59 | 0.77 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 157 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YZ5 · Crystal Structure of Streptococcus pneumoniae NanC, in complex with 3-Sialyllactose · 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 Q97Q99
- Elsewhere: RCSB PDB 4YZ5 · PDBe 4YZ5 · UniProt Q97Q99
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