Research workbench
Crystal structure of NH3-dependent NAD+ synthetase from helicobacter pylori
Analyse Crystal structure of NH3-dependent NAD+ synthetase from helicobacter pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XNG
- Type
- protein
- Length
- 517 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NH(3)-dependent NAD(+) synthetase
- EC
- 6.3.1.5
- UniProt
- O25096
- Ligands
- DND, ATP, MG
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 255 | 56% helix, 7% strand | O25096 |
| B | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 262 | 55% helix, 7% strand | O25096 |
Ligands and binding sites
- DND · Nicotinic acid adenine dinucleotide · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.86 | 0.89 | 111 | DND, MG, ATP |
| 2 | 406 | 0.82 | 0.91 | 55 | MG, DND, ATP |
| 3 | 138 | 0.42 | 0.75 | 17 | empty |
| 4 | 91 | 0.36 | 0.75 | 17 | empty |
| 5 | 78 | 0.33 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2301 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1XNG · Crystal Structure of NH3-dependent NAD+ synthetase from Helicobacter pylori · the same entry in another collection · chain A against A, TM-score 1.00
- O25096 · AlphaFold monomer V2.0 prediction for NH(3)-dependent NAD(+) synthetase (O25096) · 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 O25096
- Elsewhere: RCSB PDB 1XNG · PDBe 1XNG · UniProt O25096
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