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1.9 ångström resolution crystal structure of a NAD synthetase (nade) from salmonella typhimurium LT2 in complex with NAD(+)
Analyse 1.9 ångström resolution crystal structure of a NAD synthetase (nade) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HMQ
- Type
- protein
- Length
- 262 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NH(3)-dependent NAD(+) synthetase
- EC
- 6.3.1.5
- UniProt
- Q8ZPU5
- Ligands
- NAD, SO4
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 262 | 52% helix, 9% strand | Q8ZPU5 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- SO4 · Sulfate ion · ion · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.59 | 0.77 | 49 | SO4 |
| 2 | 105 | 0.39 | 0.76 | 25 | empty |
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 3HMQ · 1.9 Angstrom resolution crystal structure of a NAD synthetase (nadE) from Salmonella… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZPU5 · AlphaFold monomer V2.0 prediction for NH(3)-dependent NAD(+) synthetase (Q8ZPU5) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8ZPU5
- Elsewhere: RCSB PDB 3HMQ · PDBe 3HMQ · UniProt Q8ZPU5
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