Research workbench
Human PARP16 (ARTD15) in complex with carba-NAD
Analyse Human PARP16 (ARTD15) in complex with carba-NAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HXS
- Type
- protein
- Length
- 715 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mono [ADP-ribose] polymerase PARP16
- EC
- 2.4.2.30
- UniProt
- Q8N5Y8
- Ligands
- CNA, ADN, SO4
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mono [ADP-ribose] polymerase PARP16 (EC 2.4.2.30) | protein | 248 | 40% helix, 23% strand | Q8N5Y8 |
| B | Mono [ADP-ribose] polymerase PARP16 (EC 2.4.2.30) | protein | 234 | 41% helix, 24% strand | Q8N5Y8 |
| C | Mono [ADP-ribose] polymerase PARP16 (EC 2.4.2.30) | protein | 233 | 42% helix, 23% strand | Q8N5Y8 |
Ligands and binding sites
- CNA · Carba-nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- ADN · Adenosine · ligand · chains C
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.75 | 0.81 | 69 | GOL |
| 2 | 481 | 0.64 | 0.76 | 70 | CNA |
| 3 | 245 | 0.53 | 0.76 | 26 | empty |
| 4 | 223 | 0.52 | 0.76 | 26 | empty |
| 5 | 142 | 0.51 | 0.79 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 676 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 663 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6HXS · Human PARP16 (ARTD15) IN COMPLEX WITH CARBA-NAD · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N5Y8 · AlphaFold monomer V2.0 prediction for protein mono-ADP- ribosyltransferase PARP16 (Q8N5Y8) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q8N5Y8
- Elsewhere: RCSB PDB 6HXS · PDBe 6HXS · UniProt Q8N5Y8
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