Research workbench
Crystal structure of MTET3-cxxc domain in complex with 5- carboxylcytosine DNA at 1.3 ångströms resolution.
Analyse Crystal structure of MTET3-cxxc domain in complex with 5- carboxylcytosine DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EXH
- Type
- protein + DNA
- Length
- 69 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*AP*AP*TP*CP*(1CC)P*GP*GP*AP*TP*TP*C)-3'); Methylcytosine dioxygenase TET3
- EC
- 1.14.11.-
- UniProt
- L0HN04
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA (5'-D(*GP*AP*AP*TP*CP*(1CC)P*GP*GP*AP*TP*TP*C)-3') | dna | 12 | — | — |
| C | Methylcytosine dioxygenase TET3 (EC 1.14.11.-) | protein | 45 | 24% helix, 0% strand | L0HN04 |
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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.50 | 0.75 | 25 | empty |
| 2 | 117 | 0.43 | 0.77 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 520 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- A–C · 473 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 465 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5EXH · Crystal structure of mTET3-CXXC domain in complex with 5-carboxylcytosine DNA at 1.3… · the same entry in another collection · chain A against A, TM-score 1.00
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 L0HN04
- Elsewhere: RCSB PDB 5EXH · PDBe 5EXH · UniProt L0HN04
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