Research workbench
Crystal structure of class II ribonuclease H (RNase hii) with mes ligand
Analyse Crystal structure of class II ribonuclease H (RNase hii) with mes ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EKE
- Type
- protein
- Length
- 447 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease hii
- EC
- 3.1.26.4
- UniProt
- Q57599
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease hii (EC 3.1.26.4) | protein | 222 | 51% helix, 18% strand | Q57599 |
| B | Ribonuclease hii (EC 3.1.26.4) | protein | 225 | 53% helix, 19% strand | Q57599 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
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 | 211 | 0.50 | 0.76 | 25 | empty |
| 2 | 145 | 0.39 | 0.73 | 25 | empty |
| 3 | 81 | 0.32 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 541 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 1EKE · Crystal structure of class II ribonuclease H (RNase hii) with mes ligand · the same entry in another collection · chain A against A, TM-score 1.00
- Q57599 · AlphaFold monomer V2.0 prediction for ribonuclease hii (Q57599) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q57599
- Elsewhere: RCSB PDB 1EKE · PDBe 1EKE · UniProt Q57599
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