MolNFT v1 · #116477 · protein + DNA
Crystal structure of TET2-5HMC complex
5DEU · Methylcytosine dioxygenase TET2, chimeric construct: “Crystal structure of TET2-5HMC complex”. X-ray diffraction, 4 ligands (OGA, ZN, FE), 7 pockets (best druggability 0.73). MolNFT v1 #116477 on GenesisL1: 3D structure, binding…
- PDB
- 5DEU
- Type
- protein + DNA
- Length
- 436 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylcytosine dioxygenase TET2, chimeric construct; DNA…
- EC
- 1.14.11.-
- UniProt
- Q6N021
- Ligands
- OGA, ZN, FE, CL
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylcytosine dioxygenase TET2, chimeric construct (EC 1.14.11.-) | protein | 413 | 24% helix, 23% strand | Q6N021 |
| B | DNA (5'-D(*AP*CP*CP*AP*CP*(5HC)P*GP*GP*TP*GP*GP*T)-3') | dna | 12 | — | — |
| C | DNA (5'-D(P*CP*CP*AP*CP*(5HC)P*GP*GP*TP*GP*GP*T)-3') | dna | 11 | — | — |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A
- FE · Fe (III) ion · metal · chains A
- CL · Chloride ion · ion · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.73 | 0.99 | 20 | OGA, FE |
| 2 | 460 | 0.70 | 0.81 | 34 | MES |
| 3 | 510 | 0.69 | 0.79 | 52 | empty |
| 4 | 312 | 0.61 | 0.78 | 39 | empty |
| 5 | 158 | 0.54 | 0.80 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 820 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–C · 486 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–C · 469 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
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 Q6N021
- Elsewhere: RCSB PDB 5DEU · PDBe 5DEU · UniProt Q6N021
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