Research workbench
Crystal structure of NH3-dependent NAD+ synthetase from bacillus subtilis complexed with two molecules deamido-NAD
Analyse Crystal structure of NH3-dependent NAD+ synthetase from bacillus subtilis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IFX
- Type
- protein
- Length
- 490 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NH(3)-dependent NAD(+) synthetase
- EC
- 6.3.5.1
- UniProt
- P08164
- Ligands
- DND
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NH(3)-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 245 | 55% helix, 9% strand | P08164 |
Ligands and binding sites
- DND · Nicotinic acid adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.78 | 0.85 | 61 | empty |
| 2 | 328 | 0.56 | 0.76 | 36 | DND |
| 3 | 215 | 0.55 | 0.79 | 32 | empty |
| 4 | 238 | 0.55 | 0.78 | 32 | empty |
| 5 | 278 | 0.55 | 0.76 | 30 | DND |
Interfaces
1 interface between chains.
- A–B · 2717 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1IFX · Crystal structure of NH3-dependent NAD+ synthetase from bacillus subtilis complexed 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 1IFX · PDBe 1IFX · UniProt P08164
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