MolNFT v1 · #50067 · protein
Crystal structure of ribonuclease II family protein from deinococcus radiodurans, triclinic crystal form. northeast structural genomics target DRR63
2R7D: “Crystal structure of ribonuclease II family protein from deinococcus radiodurans, triclinic crystal form.…”. X-ray diffraction, 1 ligand (MG), 10 pockets (best druggability 0.76). MolNFT v1 #50067 on GenesisL1: 3D structure, binding…
- 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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