Research workbench
Crystal structure of streptococcus pneumoniae nanc, complex with NEU5AC and NEU5AC2EN following soaking with 3'SL
Analyse Crystal structure of streptococcus pneumoniae nanc, complex with NEU5AC and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YW1
- Type
- protein
- Length
- 1,318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase C
- EC
- 3.2.1.18
- UniProt
- A0A0H2UQE4
- Ligands
- DAN, SIA, PO4
- Pockets
- 17 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuraminidase C (EC 3.2.1.18) | protein | 659 | 4% helix, 45% strand | A0A0H2UQE4 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · chains B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.67 | 0.97 | 18 | empty |
| 2 | 446 | 0.65 | 0.78 | 31 | empty |
| 3 | 220 | 0.64 | 0.83 | 33 | DAN |
| 4 | 233 | 0.54 | 0.77 | 28 | PO4 |
| 5 | 226 | 0.54 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 274 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4YW1 · Crystal Structure of Streptococcus pneumoniae NanC, complex with Neu5Ac and Neu5Ac2en… · 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 A0A0H2UQE4
- Elsewhere: RCSB PDB 4YW1 · PDBe 4YW1 · UniProt A0A0H2UQE4
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