MolNFT v1 · #183077 · protein + DNA
Human TET2 in complex with unfavourable DNA substrate.
7NE6 · Methylcytosine dioxygenase TET2: “Human TET2 in complex with unfavourable DNA substrate.”. X-ray diffraction, 3 ligands (OGA, ZN, MN), 7 pockets (best druggability 0.74). MolNFT v1 #183077 on GenesisL1: 3D structure, binding sites…
- PDB
- 7NE6
- Type
- protein + DNA
- Length
- 441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylcytosine dioxygenase TET2; DNA (5'-D(*AP*CP*AP*GP*GP*(5CM)P*GP*CP*CP*TP*G)-3')
- EC
- 1.14.11.-
- UniProt
- Q6N021
- Ligands
- OGA, ZN, MN
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylcytosine dioxygenase TET2 (EC 1.14.11.-) | protein | 418 | 25% helix, 23% strand | Q6N021 |
| B | DNA (5'-D(*AP*CP*AP*GP*GP*(5CM)P*GP*CP*CP*TP*G)-3') | dna | 11 | — | — |
| C | DNA (5'-D(*AP*CP*AP*GP*GP*(5CM)P*GP*CP*CP*TP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A
- MN · Manganese (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A, B
- 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 | 62 | 0.74 | 0.99 | 20 | OGA, MN |
| 2 | 457 | 0.71 | 0.82 | 29 | MES |
| 3 | 461 | 0.67 | 0.79 | 48 | EDO |
| 4 | 323 | 0.59 | 0.77 | 35 | empty |
| 5 | 146 | 0.50 | 0.79 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 850 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 500 Ų buried · 2 hydrogen bonds · protein-nucleic
- B–C · 484 Ų buried · 48 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 7NE6 · PDBe 7NE6 · UniProt Q6N021
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