Research workbench
Structure of NAD+ synthetase from deinococcus radiodurans
Analyse Structure of NAD+ synthetase from deinococcus radiodurans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q16
- Type
- protein
- Length
- 1,064 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NH(3)-dependent NAD(+) synthetase
- EC
- 6.3.1.5
- UniProt
- Q9RYV5
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 270 | 53% helix, 8% strand | Q9RYV5 |
| B | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 268 | 51% helix, 7% strand | Q9RYV5 |
| C | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 255 | 51% helix, 8% strand | Q9RYV5 |
| D | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 271 | 51% helix, 8% strand | Q9RYV5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.79 | 0.81 | 88 | SO4 |
| 2 | 483 | 0.78 | 0.85 | 60 | empty |
| 3 | 477 | 0.77 | 0.85 | 57 | empty |
| 4 | 1144 | 0.76 | 0.79 | 91 | SO4 |
| 5 | 447 | 0.64 | 0.77 | 52 | SO4 |
Interfaces
4 interfaces between chains.
- A–B · 2603 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2581 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 195 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 104 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4Q16 · Structure of NAD+ Synthetase from Deinococcus radiodurans · the same entry in another collection · chain D against D, TM-score 1.00
- Q9RYV5 · AlphaFold monomer V2.0 prediction for NH(3)-dependent NAD(+) synthetase (Q9RYV5) · a predicted model of the same protein · chain C 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 Q9RYV5
- Elsewhere: RCSB PDB 4Q16 · PDBe 4Q16 · UniProt Q9RYV5
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