Research workbench
Bacillus nanornase a (H103A) + 2 divalent cations + PO4 at the active site
Analyse Bacillus nanornase a (H103A) + 2 divalent cations + PO4 at the active site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IZO
- Type
- protein
- Length
- 1,242 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional oligoribonuclease and pap phosphatase nrna
- EC
- 3.1.-.-, 3.1.3.7
- UniProt
- O34600
- Ligands
- MN, PO4
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional oligoribonuclease and pap phosphatase nrna (EC 3.1.-.-, 3.1.3.7) | protein | 292 | 41% helix, 10% strand | O34600 |
| B | Bifunctional oligoribonuclease and pap phosphatase nrna (EC 3.1.-.-, 3.1.3.7) | protein | 320 | 46% helix, 18% strand | O34600 |
| C, D | Bifunctional oligoribonuclease and pap phosphatase nrna (EC 3.1.-.-, 3.1.3.7) | protein | 315 | 46% helix, 19% strand | O34600 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.73 | 0.82 | 54 | empty |
| 2 | 670 | 0.63 | 0.73 | 59 | empty |
| 3 | 113 | 0.51 | 0.81 | 27 | empty |
| 4 | 234 | 0.48 | 0.74 | 36 | empty |
| 5 | 141 | 0.39 | 0.74 | 25 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1733 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 736 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 364 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 326 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5IZO · Bacillus NanoRNase A (H103A) + 2 divalent cations + PO4 at the active site · the same entry in another collection · chain D against D, TM-score 1.00
- O34600 · AlphaFold monomer V2.0 prediction for bifunctional oligoribonuclease and pap phosphatase… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O34600
- Elsewhere: RCSB PDB 5IZO · PDBe 5IZO · UniProt O34600
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