Research workbench
High resolution crystal structures of streptococcus pneumoniae nicotinamidase with trapped intermediates provide insights into catalytic mechanism and inhibition by aldehydes
Analyse High resolution crystal structures of streptococcus pneumoniae nicotinamidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O90
- Type
- protein
- Length
- 740 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamidase
- UniProt
- Q97PM2
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Nicotinamidase | protein | 187 | 38% helix, 24% strand | Q97PM2 |
| B | Nicotinamidase | protein | 189 | 37% helix, 23% strand | Q97PM2 |
| C | Nicotinamidase | protein | 177 | 37% helix, 25% strand | Q97PM2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.86 | 0.87 | 86 | empty |
| 2 | 447 | 0.66 | 0.78 | 52 | empty |
| 3 | 359 | 0.59 | 0.76 | 46 | empty |
| 4 | 236 | 0.56 | 0.78 | 44 | empty |
| 5 | 106 | 0.56 | 0.84 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–D · 941 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 898 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 658 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 505 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 379 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3O90 · High resolution crystal structures of Streptococcus pneumoniae nicotinamidase with… · 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 Q97PM2
- Elsewhere: RCSB PDB 3O90 · PDBe 3O90 · UniProt Q97PM2
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