MolNFT v1 · #78608 · protein
Human POLY(ADP-ribose) polymerase 14 (PARP14/ARTD8) - catalytic domain in complex with 6(5H)-phenanthridinone
3SE2 · Poly [ADP-ribose] polymerase 14: “Human POLY(ADP-ribose) polymerase 14 (PARP14/ARTD8) - catalytic domain in complex with 6(5H)-phenanthridinone”. X-ray diffraction, 4 ligands (LDR, 3AB, SCN), 10 pockets (best druggability 0.82).…
- PDB
- 3SE2
- Type
- protein
- Length
- 751 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly [ADP-ribose] polymerase 14
- EC
- 2.4.2.30
- UniProt
- Q460N5
- Ligands
- LDR, 3AB, SCN, CL
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 14 (EC 2.4.2.30) | protein | 186 | 27% helix, 31% strand | Q460N5 |
| B | Poly [ADP-ribose] polymerase 14 (EC 2.4.2.30) | protein | 187 | 25% helix, 31% strand | Q460N5 |
| C, D | Poly [ADP-ribose] polymerase 14 (EC 2.4.2.30) | protein | 189 | 25% helix, 37% strand | Q460N5 |
Ligands and binding sites
- LDR · phenanthridin-6(5H)-one · ligand · 2 copies · chains A, B
- 3AB · 3-aminobenzamide · ligand · 2 copies · chains C, D
- SCN · Thiocyanate ion · ion · 3 copies · chains B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, C, B, D
- GOL · Glycerol · additive · 4 copies · chains A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.82 | 0.83 | 77 | CL |
| 2 | 124 | 0.69 | 0.91 | 24 | empty |
| 3 | 137 | 0.68 | 0.89 | 24 | GOL |
| 4 | 223 | 0.64 | 0.83 | 51 | empty |
| 5 | 275 | 0.63 | 0.81 | 47 | LDR |
Interfaces
6 interfaces between chains.
- A–C · 908 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 859 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 558 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 543 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 190 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3SE2 · Human poly(ADP-ribose) polymerase 14 (PARP14/ARTD8) - catalytic domain in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q460N5 · AlphaFold monomer V2.0 prediction for protein mono-ADP- ribosyltransferase PARP14 (Q460N5) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q460N5
- Elsewhere: RCSB PDB 3SE2 · PDBe 3SE2 · UniProt Q460N5
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