Research workbench
Crystal structure of RNase H/RNA/PS-aso complex at an atomic level
Analyse Crystal structure of RNase H/RNA/PS-aso complex at an atomic level in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VRD
- Type
- protein + RNA
- Length
- 189 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease H1; RNA (5'- R(*UP*GP*GP*CP*GP*AP*GP*UP*GP*GP*GP*UP*GP*AP*GP*UP*GP*AP*GP*G)-3…
- EC
- 3.1.26.4
- UniProt
- O60930
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease H1 (EC 3.1.26.4) | protein | 149 | 40% helix, 23% strand | O60930 |
| B | RNA (5'- R(*UP*GP*GP*CP*GP*AP*GP*UP*GP*GP*GP*UP*GP*AP*GP*UP*GP*AP*GP*G)-3') | rna | 20 | — | — |
| C | RNA (5'-R(*(OMC)P*(N7X)P*(T39)P*(C5L)P*(A2M))-D(P*(SC) P*(PST)P*(SC)P*(AS)P*(SC)P*(SC)P*(SC)P*(AS)P*(SC)P*(PST))-R(P*(6OO) P*(RFJ)P*(6OO)P*(6OO)P*(6NW))-3') | rna | 20 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, B
- GOL · Glycerol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.59 | 0.75 | 27 | PEG |
| 2 | 52 | 0.25 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1005 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- A–C · 619 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–B · 607 Ų buried · 24 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 20 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 O60930
- Elsewhere: RCSB PDB 6VRD · PDBe 6VRD · UniProt O60930
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