Research workbench
Thermovibrio ammonificans RNase H3 in complex with 19-mer RNA/DNA
Analyse Thermovibrio ammonificans RNase H3 in complex with 19-mer RNA/DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PY5
- Type
- protein + DNA + RNA
- Length
- 305 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease; 5'-R(*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP *C)-3'…
- EC
- 3.1.26.-
- UniProt
- E8T217
- Ligands
- MG, SO4
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease (EC 3.1.26.-) | protein | 267 | 49% helix, 21% strand | E8T217 |
| B | 5'-R(*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP *C)-3' | rna | 19 | — | — |
| C | 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP *C)-3' | dna | 19 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, C, B
- GOL · Glycerol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.66 | 0.75 | 59 | empty |
| 2 | 114 | 0.45 | 0.79 | 22 | SO4 |
Interfaces
3 interfaces between chains.
- B–C · 924 Ų buried · 96 hydrogen bonds · nucleic-nucleic
- A–B · 893 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–C · 747 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4PY5 · Thermovibrio ammonificans RNase H3 in complex with 19-mer RNA/DNA · the same entry in another collection · 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 E8T217
- Elsewhere: RCSB PDB 4PY5 · PDBe 4PY5 · UniProt E8T217
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