Research workbench
Bacillus nanornase a active site mutant bound to pap
Analyse Bacillus nanornase a active site mutant bound to pap in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IUF
- Type
- protein
- Length
- 1,258 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional oligoribonuclease and pap phosphatase nrna
- EC
- 3.1.3.7
- UniProt
- O34600
- Ligands
- A3P
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Bifunctional oligoribonuclease and pap phosphatase nrna (EC 3.1.3.7) | protein | 314 | 45% helix, 17% strand | O34600 |
| B, D | Bifunctional oligoribonuclease and pap phosphatase nrna (EC 3.1.3.7) | protein | 315 | 45% helix, 19% strand | O34600 |
Ligands and binding sites
- A3P · Adenosine-3'-5'-diphosphate · ligand · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.69 | 0.81 | 51 | empty |
| 2 | 918 | 0.68 | 0.73 | 86 | empty |
| 3 | 975 | 0.67 | 0.73 | 78 | A3P |
| 4 | 258 | 0.51 | 0.75 | 39 | empty |
| 5 | 199 | 0.46 | 0.75 | 31 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1662 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 787 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 332 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 264 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5IUF · Bacillus NanoRNase A active site mutant bound to pAp · the same entry in another collection · chain A against A, TM-score 1.00
- O34600 · AlphaFold monomer V2.0 prediction for bifunctional oligoribonuclease and pap phosphatase… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 5IUF · PDBe 5IUF · UniProt O34600
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