Research workbench
Crystal structure of a psychrotrophic rnasehi variant with sextuple thermostabilizing mutations
Analyse Crystal structure of a psychrotrophic rnasehi variant with sextuple… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZQB
- Type
- protein
- Length
- 599 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease hi
- EC
- 3.1.26.4
- UniProt
- Q8EE30
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease hi (EC 3.1.26.4) | protein | 149 | 36% helix, 32% strand | Q8EE30 |
| B | Ribonuclease hi (EC 3.1.26.4) | protein | 147 | 38% helix, 32% strand | Q8EE30 |
| C | Ribonuclease hi (EC 3.1.26.4) | protein | 151 | 38% helix, 32% strand | Q8EE30 |
| D | Ribonuclease hi (EC 3.1.26.4) | protein | 152 | 36% helix, 31% strand | Q8EE30 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.75 | 0.81 | 61 | empty |
| 2 | 587 | 0.73 | 0.80 | 65 | empty |
| 3 | 232 | 0.69 | 0.86 | 30 | empty |
| 4 | 291 | 0.65 | 0.81 | 40 | empty |
| 5 | 237 | 0.51 | 0.76 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–B · 746 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 738 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 290 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 230 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2ZQB · Crystal structure of a psychrotrophic RNaseHI variant with sextuple thermostabilizing… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8EE30 · AlphaFold monomer V2.0 prediction for ribonuclease hi (Q8EE30) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8EE30
- Elsewhere: RCSB PDB 2ZQB · PDBe 2ZQB · UniProt Q8EE30
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