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Structure of streptococcus pneumonia nana bound with inhibitor 9N3NEU5AC2EN
Analyse Structure of streptococcus pneumonia nana bound with inhibitor 9N3NEU5AC2EN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KKY
- Type
- protein
- Length
- 941 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase a
- EC
- 3.2.1.18
- UniProt
- P62575
- Ligands
- 6UD, CL
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sialidase a (EC 3.2.1.18) | protein | 471 | 6% helix, 45% strand | P62575 |
| B | Sialidase a (EC 3.2.1.18) | protein | 470 | 5% helix, 45% strand | P62575 |
Ligands and binding sites
- 6UD · 5-acetamido-2,6-anhydro-3,5,9-trideoxy-9-triazan-1-yl-D-glycero-D-galacto-non-2-enonic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.75 | 0.78 | 107 | empty |
| 2 | 297 | 0.62 | 0.80 | 36 | empty |
| 3 | 295 | 0.62 | 0.80 | 34 | empty |
| 4 | 151 | 0.59 | 0.83 | 21 | 6UD |
| 5 | 143 | 0.58 | 0.83 | 23 | 6UD |
Interfaces
1 interface between chains.
- A–B · 1289 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
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 P62575
- Elsewhere: RCSB PDB 5KKY · PDBe 5KKY · UniProt P62575
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