MolNFT v1 · #142008 · protein
Side-ubi-NAD
5ZQ7: “Side-ubi-NAD”. X-ray diffraction, 2 ligands (NAD, AMP), 20 pockets (best druggability 0.75). MolNFT v1 #142008 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZQ7
- Type
- protein
- Length
- 1,804 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Side; Ubiquitin
- UniProt
- Q6RCR1, P0CG48
- Ligands
- NAD, AMP
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Side | protein | 828 | 53% helix, 10% strand | Q6RCR1 |
| B, D | Ubiquitin | protein | 76 | 20% helix, 34% strand | P0CG48 |
| C | Side | protein | 824 | 52% helix, 9% strand | Q6RCR1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B, D, C
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.75 | 0.86 | 44 | empty |
| 2 | 818 | 0.75 | 0.80 | 81 | NAD |
| 3 | 327 | 0.75 | 0.86 | 49 | empty |
| 4 | 723 | 0.74 | 0.80 | 66 | NAD |
| 5 | 355 | 0.60 | 0.77 | 39 | AMP |
Interfaces
3 interfaces between chains.
- A–C · 2806 Ų buried · 25 hydrogen bonds · protein-protein
- D–C · 1060 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1000 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 5ZQ7 · SidE-Ubi-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 Q6RCR1
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 5ZQ7 · PDBe 5ZQ7 · UniProt Q6RCR1 · UniProt P0CG48
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