Research workbench
The pairing geometry of the hydrophobic thymine analog 2,4- difluorotoluene in duplex DNA as analyzed by X-ray crystallography
Analyse The pairing geometry of the hydrophobic thymine analog 2,4- difluorotoluene in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I8D
- Type
- protein + DNA
- Length
- 288 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease H; 5'-D(*CP*GP*CP*GP*AP*AP*TP*(DFT)P*CP*GP*CP*G)-3'
- EC
- 3.1.26.4
- UniProt
- Q9KEI9
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ribonuclease H (EC 3.1.26.4) | protein | 132 | 36% helix, 24% strand | Q9KEI9 |
| B, D | 5'-D(*CP*GP*CP*GP*AP*AP*TP*(DFT)P*CP*GP*CP*G)-3' | dna | 12 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.44 | 0.83 | 14 | empty |
| 2 | 69 | 0.42 | 0.81 | 13 | empty |
| 3 | 53 | 0.32 | 0.77 | 9 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 327 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 313 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 86 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3I8D · The Pairing Geometry of the Hydrophobic Thymine Analog 2,4-Difluorotoluene in Duplex DNA… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KEI9 · AlphaFold monomer V2.0 prediction for ribonuclease H (Q9KEI9) · 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 Q9KEI9
- Elsewhere: RCSB PDB 3I8D · PDBe 3I8D · UniProt Q9KEI9
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