Research workbench
Structure of the catalytic domain of tankyrase 1 in complex with veliparib
Analyse Structure of the catalytic domain of tankyrase 1 in complex with veliparib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KKQ
- Type
- protein
- Length
- 824 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly [ADP-ribose] polymerase
- EC
- 2.4.2.-
- UniProt
- Q59FX0
- Ligands
- 78P, ZN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase (EC 2.4.2.-) | protein | 209 | 23% helix, 27% strand | Q59FX0 |
| B | Poly [ADP-ribose] polymerase (EC 2.4.2.-) | protein | 203 | 23% helix, 29% strand | Q59FX0 |
| C | Poly [ADP-ribose] polymerase (EC 2.4.2.-) | protein | 206 | 24% helix, 29% strand | Q59FX0 |
| D | Poly [ADP-ribose] polymerase (EC 2.4.2.-) | protein | 206 | 23% helix, 29% strand | Q59FX0 |
Ligands and binding sites
- 78P · (2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.81 | 0.82 | 91 | empty |
| 2 | 265 | 0.64 | 0.81 | 30 | 78P |
| 3 | 357 | 0.63 | 0.78 | 33 | 78P |
| 4 | 245 | 0.62 | 0.81 | 30 | 78P |
| 5 | 231 | 0.60 | 0.80 | 30 | 78P |
Interfaces
3 interfaces between chains.
- A–C · 742 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 267 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 186 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7KKQ · Structure of the catalytic domain of tankyrase 1 in complex with veliparib · the same entry in another collection · chain D against D, 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 Q59FX0
- Elsewhere: RCSB PDB 7KKQ · PDBe 7KKQ · UniProt Q59FX0
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