Research workbench
PARP15 catalytic domain in complex with 4-(3-carbamoylphenoxy) benzamide.
Analyse PARP15 catalytic domain in complex with 4-(3-carbamoylphenoxy) benzamide. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RY4
- Type
- protein
- Length
- 394 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein mono-ADP-ribosyltransferase PARP15
- EC
- 2.4.2.-
- UniProt
- Q460N3
- Ligands
- KMW
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein mono-ADP-ribosyltransferase PARP15 (EC 2.4.2.-) | protein | 197 | 23% helix, 29% strand | Q460N3 |
Ligands and binding sites
- KMW · 3-(4-aminocarbonylphenoxy)benzamide · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.78 | 0.90 | 32 | empty |
| 2 | 262 | 0.76 | 0.89 | 31 | empty |
| 3 | 318 | 0.71 | 0.84 | 43 | KMW |
| 4 | 186 | 0.61 | 0.82 | 27 | DMS |
| 5 | 122 | 0.40 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1091 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6RY4 · PARP15 catalytic domain in complex with 4-(3-carbamoylphenoxy)benzamide. · the same entry in another collection · chain A against A, TM-score 1.00
- Q460N3 · AlphaFold monomer V2.0 prediction for protein mono-ADP- ribosyltransferase PARP15 (Q460N3) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q460N3
- Elsewhere: RCSB PDB 6RY4 · PDBe 6RY4 · UniProt Q460N3
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