MolNFT v1 · #144922 · protein
Crystal structure of NAD synthetase (nade) from enterococcus faecalis in complex with NAD+
6C8Q · NH(3)-dependent NAD(+) synthetase: “Crystal structure of NAD synthetase (nade) from enterococcus faecalis in complex with NAD+”. X-ray diffraction, 1 ligand (NAD), 20 pockets (best druggability 0.78). MolNFT v1 #144922 on GenesisL1…
- PDB
- 6C8Q
- Type
- protein
- Length
- 2,122 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NH(3)-dependent NAD(+) synthetase
- EC
- 6.3.1.5
- UniProt
- Q830Y9
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 268 | 51% helix, 8% strand | Q830Y9 |
| B | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 266 | 53% helix, 8% strand | Q830Y9 |
| C | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 265 | 53% helix, 8% strand | Q830Y9 |
| D | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 264 | 54% helix, 7% strand | Q830Y9 |
| E | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 263 | 54% helix, 8% strand | Q830Y9 |
| F | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 264 | 53% helix, 8% strand | Q830Y9 |
| G | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 265 | 52% helix, 8% strand | Q830Y9 |
| H | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 267 | 52% helix, 8% strand | Q830Y9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, G, D, F, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.78 | 0.85 | 47 | NAD |
| 2 | 675 | 0.78 | 0.83 | 78 | NAD |
| 3 | 549 | 0.77 | 0.84 | 46 | NAD |
| 4 | 672 | 0.77 | 0.82 | 55 | NAD |
| 5 | 362 | 0.74 | 0.85 | 45 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2552 Ų buried · 24 hydrogen bonds · protein-protein
- C–G · 2549 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 2542 Ų buried · 24 hydrogen bonds · protein-protein
- E–H · 2515 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 701 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6C8Q · Crystal structure of NAD synthetase (NadE) from Enterococcus faecalis in complex with NAD+ · the same entry in another collection · chain H against H, TM-score 1.00
- Q830Y9 · AlphaFold monomer V2.0 prediction for NH(3)-dependent NAD(+) synthetase (Q830Y9) · a predicted model of the same protein · chain E 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 Q830Y9
- Elsewhere: RCSB PDB 6C8Q · PDBe 6C8Q · UniProt Q830Y9
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