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Crystal structure of TET2-DNA complex
Analyse Crystal structure of TET2-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NM6
- Type
- protein + DNA
- Length
- 428 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylcytosine dioxygenase TET2; 5'-D(*AP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*T)-3'
- EC
- 1.14.11.-
- UniProt
- Q6N021
- Ligands
- OGA, ZN, FE2
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylcytosine dioxygenase TET2 (EC 1.14.11.-) | protein | 407 | 25% helix, 24% strand | Q6N021 |
| B | 5'-D(*AP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*T)-3' | dna | 11 | — | — |
| C | 5'-D(*AP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*T)-3' | dna | 10 | — | — |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A
- FE2 · Fe (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.75 | 0.82 | 40 | empty |
| 2 | 68 | 0.74 | 0.98 | 20 | FE2, OGA |
| 3 | 413 | 0.67 | 0.80 | 37 | empty |
| 4 | 425 | 0.64 | 0.78 | 54 | empty |
| 5 | 154 | 0.56 | 0.82 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 810 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 479 Ų buried · 1 hydrogen bond · protein-nucleic
- B–C · 432 Ų buried · 36 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 4NM6 · PDBe 4NM6 · UniProt Q6N021
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