Research workbench
The crystal structure of PYRAZINAMIDASE/NICOTINAMIDASE from streptococcus mutans UA159
Analyse The crystal structure of PYRAZINAMIDASE/NICOTINAMIDASE from streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S2S
- Type
- protein
- Length
- 727 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative PYRAZINAMIDASE/NICOTINAMIDASE
- EC
- 3.5.1.19
- UniProt
- Q8DSG2
- Ligands
- CAD, ZN
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative PYRAZINAMIDASE/NICOTINAMIDASE (EC 3.5.1.19) | protein | 182 | 38% helix, 24% strand | Q8DSG2 |
| D | Putative PYRAZINAMIDASE/NICOTINAMIDASE (EC 3.5.1.19) | protein | 181 | 40% helix, 23% strand | Q8DSG2 |
Ligands and binding sites
- CAD · Cacodylic acid · ligand · 4 copies · chains A, B, C, D
- 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
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.87 | 0.88 | 66 | empty |
| 2 | 521 | 0.68 | 0.79 | 59 | empty |
| 3 | 552 | 0.66 | 0.77 | 57 | empty |
| 4 | 217 | 0.60 | 0.81 | 49 | empty |
| 5 | 139 | 0.56 | 0.82 | 26 | CAD |
Interfaces
6 interfaces between chains.
- A–D · 982 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 960 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 742 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 732 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 334 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3S2S · The crystal structure of pyrazinamidase/nicotinamidase from streptococcus mutans UA159 · 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 Q8DSG2
- Elsewhere: RCSB PDB 3S2S · PDBe 3S2S · UniProt Q8DSG2
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