MolNFT v1 · #94359 · protein + DNA
Structure of 5-chlorouracil modified A:U base pairs
4HUG · Ribonuclease H: “Structure of 5-chlorouracil modified A:U base pairs”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.68). MolNFT v1 #94359 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4HUG
- 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*(UCL)P*CP*GP*CP*G)-3')
- EC
- 3.1.26.4
- UniProt
- Q9KEI9
- Ligands
- MG
- Pockets
- 4 · best druggability 0.68
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, 26% 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*(UCL)P*CP*GP*CP*G)-3') | dna | 12 | — | — |
| E | DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*(UCL)P*CP*GP*CP*G)-3') | dna | 8 | — | — |
| F | DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*(UCL)P*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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.68 | 0.81 | 42 | MG, GOL |
| 2 | 442 | 0.58 | 0.74 | 50 | GOL |
| 3 | 188 | 0.47 | 0.76 | 24 | empty |
| 4 | 54 | 0.35 | 0.78 | 9 | empty |
Interfaces
9 interfaces between chains.
- C–D · 564 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- E–F · 380 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- A–B · 376 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 365 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 361 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 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 4HUG · PDBe 4HUG · UniProt Q9KEI9
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