Research workbench
Structure of Haemophilus influenzae NAD nucleotidase (NadN)
Analyse Structure of Haemophilus influenzae NAD nucleotidase (NadN) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZU0
- Type
- protein
- Length
- 1,067 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.001
- Source
- HAEMOPHILUS INFLUENZAE
- Molecule
- NAD nucleotidase
- EC
- 3.1.3.5
- UniProt
- Q4QNY4
- Ligands
- A12, ZN, PO4
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · resolution 2.001 · 2 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD nucleotidase (EC 3.1.3.5) | protein | 562 | 31% helix, 31% strand | Q4QNY4 |
| B | NAD nucleotidase (EC 3.1.3.5) | protein | 505 | 32% helix, 31% strand | Q4QNY4 |
Ligands and binding sites
- A12 · Phosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.68 | 0.77 | 85 | PO4, A12 |
| 2 | 694 | 0.65 | 0.75 | 78 | empty |
| 3 | 134 | 0.50 | 0.80 | 19 | empty |
| 4 | 51 | 0.48 | 0.86 | 14 | empty |
| 5 | 68 | 0.46 | 0.83 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1207 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3ZU0 · Structure of haemophilus influenzae NAD nucleotidase (nadn) · 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 Q4QNY4
- Elsewhere: RCSB PDB 3ZU0 · PDBe 3ZU0 · UniProt Q4QNY4
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