Research workbench
Crystal structure of ribonuclease II family protein from deinococcus radiodurans, triclinic crystal form. northeast structural genomics target DRR63
Analyse Crystal structure of ribonuclease II family protein from deinococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R7D
- Type
- protein
- Length
- 1,379 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease II family protein
- UniProt
- Q9RYD0
- Ligands
- MG
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease II family protein | protein | 461 | 35% helix, 25% strand | Q9RYD0 |
| B, C | Ribonuclease II family protein | protein | 459 | 35% helix, 25% strand | Q9RYD0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.76 | 0.78 | 81 | empty |
| 2 | 1166 | 0.76 | 0.78 | 88 | empty |
| 3 | 1072 | 0.76 | 0.78 | 82 | empty |
| 4 | 85 | 0.44 | 0.80 | 15 | empty |
| 5 | 71 | 0.41 | 0.80 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 197 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 190 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 184 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 2R7D · Crystal structure of ribonuclease II family protein from Deinococcus radiodurans… · 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 Q9RYD0
- Elsewhere: RCSB PDB 2R7D · PDBe 2R7D · UniProt Q9RYD0
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