MolNFT v1 · #5312 · protein
Crystal structure of NH3-dependent NAD+ synthetase from bacillus subtilis complexed with one molecule ATP, two molecules deamido-NAD+ and one MG2+ ion
1EE1 · NH(3)-dependent NAD(+) synthetase: “Crystal structure of NH3-dependent NAD+ synthetase from bacillus subtilis complexed with one molecule ATP…”. X-ray diffraction, 3 ligands (DND, ATP, MG), 4 pockets (best druggability 0.82). MolNFT…
- PDB
- 1EE1
- 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
- 6.3.5.1
- UniProt
- P08164
- Ligands
- DND, ATP, MG
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NH(3)-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 271 | 54% helix, 8% strand | P08164 |
| B | NH(3)-dependent NAD(+) synthetase (EC 6.3.5.1) | protein | 246 | 56% helix, 8% strand | P08164 |
Ligands and binding sites
- DND · Nicotinic acid adenine dinucleotide · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.82 | 0.84 | 89 | MG, DND, ATP |
| 2 | 524 | 0.78 | 0.85 | 58 | empty |
| 3 | 309 | 0.58 | 0.77 | 35 | DND |
| 4 | 204 | 0.51 | 0.77 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 2677 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1EE1 · 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 1EE1 · PDBe 1EE1 · UniProt P08164
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