MolNFT v1 · #128516 · protein
Crystal structure of TNKS2 in complex with OD334
5NSP · Tankyrase-2: “Crystal structure of TNKS2 in complex with OD334”. X-ray diffraction, 4 ligands (BCT, 97E, ZN), 4 pockets (best druggability 0.77). MolNFT v1 #128516 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5NSP
- Type
- protein
- Length
- 417 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
- BCT, 97E, ZN, SO4
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tankyrase-2 (EC 2.4.2.30) | protein | 161 | 29% helix, 25% strand | Q9H2K2 |
| C, D | Tankyrase-2 (EC 2.4.2.30) | protein | 47 | 6% helix, 43% strand | Q9H2K2 |
| B | Tankyrase-2 (EC 2.4.2.30) | protein | 162 | 29% helix, 27% strand | Q9H2K2 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, C, B, D
- 97E · 1-[4-[4-(2-chlorophenyl)-5-pyrimidin-4-yl-1,2,4-triazol-3-yl]phenyl]-2-oxidanylidene-3~{H}-benzimidazole-5-carbonitrile · ligand · chains B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · chains C
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 | 451 | 0.77 | 0.85 | 61 | SO4 |
| 2 | 395 | 0.71 | 0.83 | 50 | SO4, 97E, BCT |
| 3 | 91 | 0.60 | 0.88 | 22 | BCT |
| 4 | 112 | 0.46 | 0.78 | 21 | empty |
Interfaces
5 interfaces between chains.
- B–D · 3191 Ų buried · 66 hydrogen bonds · protein-protein
- A–C · 3077 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 601 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 68 Ų buried · 0 hydrogen bonds · protein-protein
- C–B · 56 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5NSP · Crystal structure of TNKS2 in complex with OD334 · 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 5NSP · PDBe 5NSP · UniProt Q9H2K2
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