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Human TET2 in complex with favourable DNA substrate.
Analyse Human TET2 in complex with favourable DNA substrate. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NE3
- Type
- protein + DNA
- Length
- 439 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, FE2
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylcytosine dioxygenase TET2 (EC 1.14.11.-) | protein | 416 | 24% 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
- FE2 · Fe (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C, 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 | 58 | 0.72 | 0.99 | 20 | FE2, OGA |
| 2 | 479 | 0.72 | 0.82 | 32 | MES |
| 3 | 474 | 0.66 | 0.78 | 51 | EDO |
| 4 | 284 | 0.57 | 0.77 | 33 | empty |
| 5 | 151 | 0.53 | 0.80 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 854 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–C · 488 Ų buried · 2 hydrogen bonds · protein-nucleic
- B–C · 473 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 7NE3 · PDBe 7NE3 · UniProt Q6N021
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