Research workbench
Structure of 5-chlorouracil modified G:U base pair
Analyse Structure of 5-chlorouracil modified G:U base pair in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HUE
- Type
- protein + DNA
- Length
- 308 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease H; DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(UCL)P*GP*CP*G)-3')
- EC
- 3.1.26.4
- UniProt
- Q9KEI9
- Ligands
- MG
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonuclease H (EC 3.1.26.4) | protein | 134 | 35% helix, 25% strand | Q9KEI9 |
| C, D | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(UCL)P*GP*CP*G)-3') | dna | 12 | — | — |
| E | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(UCL)P*GP*CP*G)-3') | dna | 8 | — | — |
| F | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(UCL)P*GP*CP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, E
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.67 | 0.81 | 40 | MG, GOL |
| 2 | 437 | 0.59 | 0.75 | 52 | GOL |
| 3 | 226 | 0.52 | 0.77 | 26 | empty |
| 4 | 50 | 0.32 | 0.77 | 10 | empty |
| 5 | 61 | 0.25 | 0.72 | 15 | empty |
Interfaces
9 interfaces between chains.
- C–D · 567 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–B · 387 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 381 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- A–C · 361 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–E · 361 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 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 Q9KEI9
- Elsewhere: RCSB PDB 4HUE · PDBe 4HUE · UniProt Q9KEI9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.