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Crystal structure of bacillus halodurans ribonuclease H1 in complex with an RNA/DNA hybrid: reaction in 5 mm MG2+ and 200 mm rb+ for 360 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
- 6DOX
- Type
- protein + DNA + RNA
- Length
- 148 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease H; 5'-R(*AP*CP*AP*U)-3' portion of cleaved RNA 5'- R(*AP*CP*AP*UP*CP*G)-3'…
- EC
- 3.1.26.4
- UniProt
- Q9KEI9
- Ligands
- RB, MG, CL
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease H (EC 3.1.26.4) | protein | 136 | 35% helix, 26% strand | Q9KEI9 |
| B | 5'-R(*AP*CP*AP*U)-3' portion of cleaved RNA 5'- R(*AP*CP*AP*UP*CP*G)-3' | rna | 4 | — | — |
| b | 5'-R(P*CP*G)-3' portion of cleaved RNA 5'- R(*AP*CP*AP*UP*CP*G)-3' | rna | 2 | — | — |
| C | DNA (5'-D(*CP*GP*AP*TP*GP*T)-3') | dna | 6 | — | — |
Ligands and binding sites
- RB · Rubidium ion · metal · 5 copies · chains A, b, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, b, B
- CL · Chloride ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C
- GOL · Glycerol · additive · 5 copies · chains A, b, C
- PEG · Di(hydroxyethyl)ether · 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 | 0.34 | 0.78 | 11 | CL, GOL |
Interfaces
6 interfaces between chains.
- A–C · 425 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–b · 319 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–B · 272 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 187 Ų buried · 14 hydrogen bonds · nucleic-nucleic
- b–C · 146 Ų buried · 10 hydrogen bonds · nucleic-nucleic
Compared structures
- 6DOX · 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 6DOX · PDBe 6DOX · UniProt Q9KEI9
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