MolNFT v1 · #94358 · protein + DNA
Structure of 5-chlorouracil modified A:U base pair
4HUF · Ribonuclease H: “Structure of 5-chlorouracil modified A:U base pair”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.58). MolNFT v1 #94358 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4HUF
- Type
- protein + DNA
- Length
- 306 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*(UCL)P*TP*CP*GP*CP*G)-3')
- EC
- 3.1.26.4
- UniProt
- Q9KEI9
- Ligands
- MG
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease H (EC 3.1.26.4) | protein | 134 | 34% helix, 25% strand | Q9KEI9 |
| B | Ribonuclease H (EC 3.1.26.4) | protein | 131 | 37% helix, 27% strand | Q9KEI9 |
| C, D | DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*TP*CP*GP*CP*G)-3') | dna | 12 | — | — |
| E | DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*TP*CP*GP*CP*G)-3') | dna | 8 | — | — |
| F | DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*TP*CP*GP*CP*G)-3') | dna | 9 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, E
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.58 | 0.79 | 28 | MG |
| 2 | 371 | 0.58 | 0.75 | 48 | GOL |
| 3 | 163 | 0.55 | 0.81 | 19 | GOL |
| 4 | 179 | 0.47 | 0.76 | 23 | empty |
| 5 | 53 | 0.33 | 0.77 | 10 | empty |
Interfaces
9 interfaces between chains.
- C–D · 564 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- A–B · 396 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 368 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- B–E · 362 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 362 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 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 4HUF · PDBe 4HUF · UniProt Q9KEI9
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