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Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 20 mM Mn2+ and 200 mM K+ for 40 s at 21 C
Analyse Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DPE
- Type
- protein + DNA + RNA
- Length
- 148 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.56
- Source
- Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 /…
- Molecule
- Ribonuclease H; RNA (5'-R(*AP*CP*AP*U)-3'); RNA (5'-R(P*CP*G)-3'); DNA…
- EC
- 3.1.26.4
- UniProt
- Q9KEI9
- Ligands
- MN, K, IOD
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · resolution 1.56 · 4 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease H (EC 3.1.26.4) | protein | 136 | 33% helix, 26% strand | Q9KEI9 |
| B | RNA (5'-R(*AP*CP*AP*U)-3') | rna | 4 | — | — |
| b | RNA (5'-R(P*CP*G)-3') | rna | 2 | — | — |
| C | DNA (5'-D(*CP*GP*AP*TP*GP*T)-3') | dna | 6 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 5 copies · chains A, b, B
- K · Potassium ion · metal · chains A, B, b
- IOD · Iodide ion · ion · 5 copies · chains A, b
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C
- GOL · Glycerol · additive · 3 copies · chains A, b, C
- PGE · Triethylene glycol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.31 | 0.77 | 10 | IOD, GOL |
Interfaces
6 interfaces between chains.
- A–C · 442 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–b · 325 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 271 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 190 Ų buried · 15 hydrogen bonds · nucleic-nucleic
- b–C · 144 Ų buried · 11 hydrogen bonds · nucleic-nucleic
Compared structures
- 6DPE · Crystal structure of bacillus halodurans ribonuclease H1 in complex with an RNA/DNA… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KEI9 · AlphaFold monomer V2.0 prediction for ribonuclease H (Q9KEI9) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 6DPE · PDBe 6DPE · UniProt Q9KEI9
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