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Crystal structure of nudix family protein with NAD
Analyse Crystal structure of nudix family protein with NAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ISY
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH pyrophosphatase
- EC
- 3.6.1.22
- UniProt
- P32664
- Ligands
- NAD, ZN
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH pyrophosphatase (EC 3.6.1.22) | protein | 253 | 21% helix, 39% strand | P32664 |
| C | NADH pyrophosphatase (EC 3.6.1.22) | protein | 249 | 21% helix, 39% strand | P32664 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.79 | 0.80 | 110 | NAD |
| 2 | 61 | 0.36 | 0.78 | 19 | empty |
| 3 | 90 | 0.36 | 0.75 | 24 | empty |
| 4 | 91 | 0.35 | 0.75 | 27 | empty |
| 5 | 54 | 0.32 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 1759 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
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 P32664
- Elsewhere: RCSB PDB 5ISY · PDBe 5ISY · UniProt P32664
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