MolNFT v1 · #121397 · protein
Crystal structure of nade from streptococcus pyogenes
5HUH · NH(3)-dependent NAD(+) synthetase: “Crystal structure of nade from streptococcus pyogenes”. X-ray diffraction, 2 ligands (MG, SO4), 3 pockets (best druggability 0.72). MolNFT v1 #121397 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5HUH
- Type
- protein
- Length
- 521 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
- A0A0H3BZ89
- Ligands
- MG, SO4
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 261 | 54% helix, 8% strand | A0A0H3BZ89 |
| B | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 260 | 53% helix, 8% strand | A0A0H3BZ89 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.72 | 0.77 | 85 | SO4, MG |
| 2 | 391 | 0.72 | 0.83 | 55 | SO4 |
| 3 | 828 | 0.72 | 0.77 | 78 | SO4, MG |
Interfaces
1 interface between chains.
- A–B · 2439 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5HUH · Crystal Structure of NadE from Streptococcus pyogenes · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0H3BZ89
- Elsewhere: RCSB PDB 5HUH · PDBe 5HUH · UniProt A0A0H3BZ89
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