Research workbench
Crystal structure of the streptococcus pyogenes NAD+ glycohydrolase spn in complex with ifs, the immunity factor for spn
Analyse Crystal structure of the streptococcus pyogenes NAD+ glycohydrolase spn in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PNT
- Type
- protein
- Length
- 821 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD+-glycohydrolase; Immunity factor for spn
- EC
- 3.2.2.5
- UniProt
- D7S065, Q2VJ58
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | NAD+-glycohydrolase (EC 3.2.2.5) | protein | 250 | 43% helix, 16% strand | D7S065 |
| B | Immunity factor for spn | protein | 161 | 61% helix, 0% strand | Q2VJ58 |
| D | Immunity factor for spn | protein | 160 | 65% helix, 0% strand | Q2VJ58 |
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.83 | 0.84 | 110 | empty |
| 2 | 611 | 0.82 | 0.87 | 62 | empty |
| 3 | 62 | 0.71 | 0.97 | 20 | empty |
| 4 | 54 | 0.71 | 0.98 | 18 | empty |
| 5 | 366 | 0.65 | 0.79 | 38 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1734 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1712 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 309 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 130 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 117 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 modified (engineered).
Compared structures
- 3PNT · Crystal Structure of the Streptococcus pyogenes NAD+ glycohydrolase SPN in complex 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 D7S065
- Every structure of UniProt Q2VJ58
- Elsewhere: RCSB PDB 3PNT · PDBe 3PNT · UniProt D7S065 · UniProt Q2VJ58
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