MolNFT v1 · #94035 · protein
Complex structure of human tankyrase 2 with apigenin
4HKK · Tankyrase-2: “Complex structure of human tankyrase 2 with apigenin”. X-ray diffraction, 3 ligands (AGI, ZN, SO4), 4 pockets (best druggability 0.77). MolNFT v1 #94035 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4HKK
- Type
- protein
- Length
- 418 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
- AGI, ZN, SO4
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tankyrase-2 (EC 2.4.2.30) | protein | 162 | 28% helix, 26% strand | Q9H2K2 |
| B, D | Tankyrase-2 (EC 2.4.2.30) | protein | 47 | 6% helix, 45% strand | Q9H2K2 |
Ligands and binding sites
- AGI · 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one · ligand · 2 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, C, D
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 | 384 | 0.77 | 0.87 | 56 | SO4, AGI |
| 2 | 248 | 0.62 | 0.81 | 37 | SO4, AGI |
| 3 | 155 | 0.52 | 0.79 | 18 | empty |
| 4 | 99 | 0.34 | 0.73 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3086 Ų buried · 65 hydrogen bonds · protein-protein
- C–D · 3072 Ų buried · 66 hydrogen bonds · protein-protein
- A–C · 627 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 103 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 47 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4HKK · Complex structure of human tankyrase 2 with apigenin · 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 4HKK · PDBe 4HKK · UniProt Q9H2K2
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