Research workbench
Bh-RNASEH:2'-sme-DNA complex
Analyse Bh-RNASEH:2'-sme-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OPK
- Type
- protein + DNA
- Length
- 290 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*(USM)P*TP*CP*GP*CP*G)-3'
- EC
- 3.1.26.4
- UniProt
- Q9KEI9
- Pockets
- 5 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ribonuclease H (EC 3.1.26.4) | protein | 133 | 35% helix, 26% strand | Q9KEI9 |
| B, D | 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*TP*CP*GP*CP*G)-3' | dna | 12 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.44 | 0.82 | 13 | empty |
| 2 | 64 | 0.43 | 0.82 | 13 | empty |
| 3 | 56 | 0.32 | 0.76 | 10 | empty |
| 4 | 55 | 0.32 | 0.76 | 12 | GOL |
| 5 | 80 | 0.29 | 0.72 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–D · 324 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–B · 306 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–C · 108 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 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 4OPK · PDBe 4OPK · UniProt Q9KEI9
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