Research workbench
NH3-dependent NAD synthetase from campylobacter jejuni subsp. jejuni nctc 11168 in complex with the nitrate ion
Analyse NH3-dependent NAD synthetase from campylobacter jejuni subsp. jejuni nctc 11168… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P52
- Type
- protein
- Length
- 458 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
- Q9PPB0
- Ligands
- NO3
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 229 | 56% helix, 10% strand | Q9PPB0 |
| B | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 229 | 56% helix, 10% strand | Q9PPB0 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 4 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.76 | 0.79 | 114 | empty |
| 2 | 284 | 0.62 | 0.80 | 40 | NO3 |
| 3 | 312 | 0.62 | 0.79 | 47 | NO3 |
| 4 | 54 | 0.34 | 0.77 | 13 | empty |
| 5 | 52 | 0.30 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2232 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 3P52 · NH3-dependent NAD synthetase from Campylobacter jejuni subsp. jejuni NCTC 11168 in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9PPB0 · AlphaFold monomer V2.0 prediction for NH(3)-dependent NAD(+) synthetase (Q9PPB0) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9PPB0
- Elsewhere: RCSB PDB 3P52 · PDBe 3P52 · UniProt Q9PPB0
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