MolNFT v1 · #162821 · protein
Characterization of an intertidal zone metagenome oligoribonuclease and the role of the intermolecular disulfide bond for homodimer formation and nuclease activity.
6RK6: “Characterization of an intertidal zone metagenome oligoribonuclease and the role of the intermolecular…”. X-ray diffraction, 1 ligand (MN), 4 pockets (best druggability 0.69). MolNFT v1 #162821 on GenesisL1: 3D structure, binding…
- 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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