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Crystal structure of VIP2 with NAD
Analyse Crystal structure of VIP2 with NAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QS2
- Type
- protein
- Length
- 401 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyltransferase
- EC
- 2.4.2.30
- Ligands
- NAD
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosyltransferase (EC 2.4.2.30) | protein | 401 | 34% helix, 30% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.64 | 0.83 | 28 | empty |
| 2 | 241 | 0.55 | 0.78 | 26 | NAD |
| 3 | 184 | 0.49 | 0.76 | 25 | empty |
| 4 | 60 | 0.33 | 0.77 | 12 | empty |
| 5 | 50 | 0.31 | 0.77 | 12 | empty |
Compared structures
- 1QS2 · Crystal structure of VIP2 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
- Elsewhere: RCSB PDB 1QS2 · PDBe 1QS2
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