Research workbench
Crystal structure of Salmo salar RidA-2
Analyse Crystal structure of Salmo salar RidA-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TCD
- Type
- protein
- Length
- 774 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.36
- Source
- Salmo salar
- Molecule
- Ribonuclease UK114
- UniProt
- C0H8I4
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · resolution 1.36 · 5 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease UK114 | protein | 127 | 28% helix, 32% strand | C0H8I4 |
| B, C | Ribonuclease UK114 | protein | 129 | 27% helix, 31% strand | C0H8I4 |
| D | Ribonuclease UK114 | protein | 133 | 27% helix, 30% strand | C0H8I4 |
| E | Ribonuclease UK114 | protein | 130 | 25% helix, 32% strand | C0H8I4 |
| F | Ribonuclease UK114 | protein | 126 | 30% helix, 32% strand | C0H8I4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains E, F, D
- ACT · Acetate ion · additive · 7 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.83 | 0.99 | 26 | empty |
| 2 | 175 | 0.83 | 0.98 | 26 | empty |
| 3 | 313 | 0.65 | 0.81 | 52 | empty |
| 4 | 61 | 0.63 | 0.92 | 16 | ACT |
| 5 | 198 | 0.59 | 0.81 | 33 | empty |
Interfaces
7 interfaces between chains.
- D–F · 1279 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1145 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1132 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1121 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1025 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6TCD · Crystal structure of salmo salar rida-2 · 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 C0H8I4
- Elsewhere: RCSB PDB 6TCD · PDBe 6TCD · UniProt C0H8I4
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