MolNFT v1 · #114699 · protein
Human tankyrase-2 in complex with macrocyclised extended peptide CP4N2M3
5BXO: “Human tankyrase-2 in complex with macrocyclised extended peptide CP4N2M3”. X-ray diffraction, 4 ligands (ACE, 4XP, SO4), 2 pockets (best druggability 0.59). MolNFT v1 #114699 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5BXO
- Type
- protein
- Length
- 339 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
- ACE, 4XP, SO4, NH2
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tankyrase-2 (EC 2.4.2.30) | protein | 160 | 52% helix, 0% strand | Q9H2K2 |
| B | Tankyrase-2 (EC 2.4.2.30) | protein | 163 | 50% helix, 0% strand | Q9H2K2 |
| C, D | Tankyrase-2 (EC 2.4.2.30) | protein | 8 | 0% helix, 0% strand | Q9H2K2 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
- 4XP · 4,4'-propane-1,3-diylbis(1-methyl-1H-1,2,3-triazole) · ligand · 2 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains C, D
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.59 | 0.76 | 53 | empty |
| 2 | 203 | 0.49 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- B–D · 588 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 587 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 450 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 5BXO · Human Tankyrase-2 in Complex with Macrocyclised Extended Peptide cp4n2m3 · 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 5BXO · PDBe 5BXO · UniProt Q9H2K2
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