MolNFT v1 · #122663 · protein
Crystal structure of E. COLI nudc in complex with NAD
5IW4 · NADH pyrophosphatase: “Crystal structure of E. COLI nudc in complex with NAD”. X-ray diffraction, 2 ligands (NAD, ZN), 4 pockets (best druggability 0.73). MolNFT v1 #122663 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5IW4
- Type
- protein
- Length
- 515 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH pyrophosphatase
- EC
- 3.6.1.22
- UniProt
- D6JHV3
- Ligands
- NAD, ZN
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH pyrophosphatase (EC 3.6.1.22) | protein | 257 | 23% helix, 39% strand | D6JHV3 |
| B | NADH pyrophosphatase (EC 3.6.1.22) | protein | 258 | 23% helix, 38% strand | D6JHV3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.73 | 0.78 | 71 | NAD |
| 2 | 707 | 0.71 | 0.78 | 72 | NAD |
| 3 | 89 | 0.40 | 0.77 | 24 | empty |
| 4 | 52 | 0.37 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1751 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5IW4 · Crystal structure of E. coli NudC in complex with NAD · 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 D6JHV3
- Elsewhere: RCSB PDB 5IW4 · PDBe 5IW4 · UniProt D6JHV3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.