Research workbench
Characterization of an intertidal zone metagenome oligoribonuclease and the role of the intermolecular disulfide bond for homodimer formation and nuclease activity.
Analyse Characterization of an intertidal zone metagenome oligoribonuclease and the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RK6
- Type
- protein
- Length
- 532 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligoribonuclease
- EC
- 3.1.13.3
- Ligands
- MN
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Oligoribonuclease (EC 3.1.13.3) | protein | 177 | 49% helix, 19% strand | — |
| C | Oligoribonuclease (EC 3.1.13.3) | protein | 178 | 49% helix, 19% strand | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.69 | 0.76 | 66 | MN |
| 2 | 705 | 0.69 | 0.76 | 75 | empty |
| 3 | 116 | 0.41 | 0.76 | 23 | empty |
| 4 | 77 | 0.40 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1480 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 376 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 34 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6RK6 · Characterization of an intertidal zone metagenome oligoribonuclease and the role of the… · 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
- Elsewhere: RCSB PDB 6RK6 · PDBe 6RK6
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