Research workbench
The structural basis for recognition of J-base containing DNA by a novel DNA-binding domain in JBP1
Analyse The structural basis for recognition of J-base containing DNA by a novel… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XSE
- Type
- protein
- Length
- 160 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymine dioxygenase JBP1
- EC
- 1.14.11.6
- UniProt
- Q9U6M1
- Ligands
- NO3
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymine dioxygenase JBP1 (EC 1.14.11.6) | protein | 160 | 72% helix, 0% strand | Q9U6M1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.35 | 0.76 | 17 | empty |
| 2 | 73 | 0.35 | 0.76 | 13 | empty |
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 2XSE · The structural basis for recognition of J-base containing DNA by a novel DNA-binding… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9U6M1 · AlphaFold monomer V2.0 prediction for thymine dioxygenase JBP1 (Q9U6M1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9U6M1
- Elsewhere: RCSB PDB 2XSE · PDBe 2XSE · UniProt Q9U6M1
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