Research workbench
Crystal structure of human tankyrase 2 in complex with 3-amino- benzamide.
Analyse Crystal structure of human tankyrase 2 in complex with 3-amino- benzamide. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PML
- Type
- protein
- Length
- 809 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tankyrase-2
- EC
- 2.4.2.30
- UniProt
- Q9H2K2
- Ligands
- 3AB, ZN
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tankyrase-2 (EC 2.4.2.30) | protein | 198 | 24% helix, 25% strand | Q9H2K2 |
| B | Tankyrase-2 (EC 2.4.2.30) | protein | 205 | 24% helix, 27% strand | Q9H2K2 |
| C | Tankyrase-2 (EC 2.4.2.30) | protein | 208 | 24% helix, 27% strand | Q9H2K2 |
| D | Tankyrase-2 (EC 2.4.2.30) | protein | 198 | 24% helix, 27% strand | Q9H2K2 |
Ligands and binding sites
- 3AB · 3-aminobenzamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, C, B
- IPA · Isopropyl alcohol · additive · chains 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 | 847 | 0.80 | 0.83 | 119 | 3AB, GOL, EDO |
| 2 | 1050 | 0.77 | 0.79 | 121 | 3AB, GOL |
| 3 | 291 | 0.63 | 0.80 | 29 | 3AB, GOL |
| 4 | 95 | 0.34 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–D · 945 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 920 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 519 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4PML · Crystal Structure of human Tankyrase 2 in complex with 3-amino-benzamide. · 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 Q9H2K2
- Elsewhere: RCSB PDB 4PML · PDBe 4PML · UniProt Q9H2K2
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