Research workbench
Crystal structure of NH3-dependent NAD+ synthetase from bacillus subtilis in complex with NAD-adenylate
Analyse Crystal structure of NH3-dependent NAD+ synthetase from bacillus subtilis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NSY
- Type
- protein
- Length
- 542 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (NAD synthetase)
- EC
- 6.3.5.1
- UniProt
- P08164
- Ligands
- AMP, NAD, POP, MG
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (NAD synthetase) (EC 6.3.5.1) | protein | 271 | 53% helix, 8% strand | P08164 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.81 | 0.84 | 90 | MG, AMP, NAD, POP |
| 2 | 896 | 0.79 | 0.82 | 90 | MG, AMP, NAD, POP |
| 3 | 483 | 0.78 | 0.86 | 61 | GOL |
Interfaces
1 interface between chains.
- A–B · 2696 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 2NSY · Crystal structure of NH3-dependent NAD+ synthetase from bacillus subtilis in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P08164 · AlphaFold monomer V2.0 prediction for NH(3)-dependent NAD(+) synthetase (P08164) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P08164
- Elsewhere: RCSB PDB 2NSY · PDBe 2NSY · UniProt P08164
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