Research workbench
B. halodurans RNase H catalytic domain E188A mutant in complex with CA2+ and RNA/DNA hybrid
Analyse B. halodurans RNase H catalytic domain E188A mutant in complex with CA2+ and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G8W
- Type
- protein + DNA + RNA
- Length
- 146 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(P*UP*CP*GP*AP*CP*A)-3'; 5'-D(*AP*TP*GP*TP*CP*G)-3'; Ribonuclease H
- EC
- 3.1.26.4
- UniProt
- Q9KEI9
- Ligands
- CA
- Pockets
- 2 · best druggability 0.32
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-R(P*UP*CP*GP*AP*CP*A)-3' | rna | 6 | — | — |
| C | 5'-D(*AP*TP*GP*TP*CP*G)-3' | dna | 6 | — | — |
| A | Ribonuclease H (EC 3.1.26.4) | protein | 134 | 35% helix, 24% strand | Q9KEI9 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.32 | 0.77 | 9 | empty |
| 2 | 79 | 0.32 | 0.74 | 14 | CA |
Interfaces
3 interfaces between chains.
- C–A · 432 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 261 Ų buried · 22 hydrogen bonds · nucleic-nucleic
- B–A · 164 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 2G8W · B. halodurans RNase H catalytic domain E188A mutant in complex with Ca2+ and RNA/DNA… · the same entry in another collection · chain B against B, 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 2G8W · PDBe 2G8W · UniProt Q9KEI9
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