MolNFT v1 · #120628 · protein
DNA targeting ADP-ribosyltransferase pierisin-1 in complex with beta- NAD+
5H6J: “DNA targeting ADP-ribosyltransferase pierisin-1 in complex with beta- NAD+”. X-ray diffraction, 1 ligand (NAD), 4 pockets (best druggability 0.58). MolNFT v1 #120628 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5H6J
- Type
- protein
- Length
- 443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pierisin-1
- EC
- 2.4.2.-
- UniProt
- H3JU00
- Ligands
- NAD
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pierisin-1 (EC 2.4.2.-) | protein | 221 | 25% helix, 24% strand | H3JU00 |
| B | Pierisin-1 (EC 2.4.2.-) | protein | 222 | 26% helix, 24% strand | H3JU00 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.58 | 0.76 | 30 | empty |
| 2 | 241 | 0.54 | 0.77 | 30 | NAD |
| 3 | 204 | 0.51 | 0.77 | 32 | NAD |
| 4 | 73 | 0.44 | 0.81 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 539 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5H6J · DNA targeting ADP-ribosyltransferase Pierisin-1 in complex with beta-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 H3JU00
- Elsewhere: RCSB PDB 5H6J · PDBe 5H6J · UniProt H3JU00
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