Research workbench
T. maritima RNase H2 in complex with nucleic acid substrate and calcium ions
Analyse T. maritima RNase H2 in complex with nucleic acid substrate and calcium ions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O3G
- Type
- protein + DNA
- Length
- 246 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease hii; DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3'); DNA/RNA…
- EC
- 3.1.26.4
- UniProt
- Q9X017
- Ligands
- CA
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease hii (EC 3.1.26.4) | protein | 222 | 50% helix, 15% strand | Q9X017 |
| C | DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3') | dna | 12 | — | — |
| D | DNA/RNA (5'-D(*GP*AP*CP*AP*C)-R(P*C)-D(P*TP*GP*AP*TP*TP*C)- 3') | dna | 12 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.54 | 0.77 | 19 | empty |
| 2 | 66 | 0.36 | 0.78 | 15 | CA |
| 3 | 55 | 0.26 | 0.74 | 10 | CA |
Interfaces
3 interfaces between chains.
- A–D · 641 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 544 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–C · 525 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 3O3G · T. maritima RNase H2 in complex with nucleic acid substrate and calcium ions · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X017 · AlphaFold monomer V2.0 prediction for ribonuclease hii (Q9X017) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9X017
- Elsewhere: RCSB PDB 3O3G · PDBe 3O3G · UniProt Q9X017
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