Research workbench
Crystal structure of TET3 in complex with a non-cpg dsdna
Analyse Crystal structure of TET3 in complex with a non-cpg dsdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HP1
- Type
- protein + DNA
- Length
- 75 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3'); LOC100036628 protein
- UniProt
- A0JP82
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA (5'-D(*GP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*C)-3') | dna | 12 | — | — |
| C | LOC100036628 protein | protein | 51 | 16% helix, 0% strand | A0JP82 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.55 | 0.77 | 29 | empty |
| 2 | 139 | 0.48 | 0.79 | 17 | empty |
| 3 | 65 | 0.32 | 0.76 | 13 | empty |
| 4 | 63 | 0.28 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 555 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- A–C · 491 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 325 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4HP1 · Crystal structure of Tet3 in complex with a non-CpG dsDNA · the same entry in another collection · chain A against A, TM-score 1.00
- A0JP82 · AlphaFold monomer V2.0 prediction for methylcytosine dioxygenase TET3 (A0JP82) · a predicted model of the same protein · chain C against A, TM-score 0.85
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 A0JP82
- Elsewhere: RCSB PDB 4HP1 · PDBe 4HP1 · UniProt A0JP82
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