Research workbench
Small RNA phage PRR1 in complex with an RNA operator fragment
Analyse Small RNA phage PRR1 in complex with an RNA operator fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ANG
- Type
- protein + RNA
- Length
- 419 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein; 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3'
- UniProt
- P03616
- Ligands
- CA
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Coat protein | protein | 131 | 16% helix, 50% strand | P03616 |
| R | 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3' | rna | 13 | — | — |
| S | 5'-R(*CP*CP*AP*UP*AP*AP*GP*GP*AP*GP*CP*UP*AP*CP *CP*UP*AP*UP*GP*GP)-3' | rna | 13 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.71 | 0.78 | 65 | empty |
| 2 | 330 | 0.64 | 0.80 | 33 | empty |
| 3 | 133 | 0.44 | 0.76 | 25 | empty |
| 4 | 113 | 0.43 | 0.77 | 20 | empty |
| 5 | 128 | 0.41 | 0.76 | 21 | empty |
Interfaces
7 interfaces between chains.
- A–B · 3598 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 435 Ų buried · 3 hydrogen bonds · protein-protein
- B–R · 426 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–R · 351 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–S · 347 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 4ANG · Small RNA phage PRR1 in complex with an RNA operator fragment · 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 P03616
- Elsewhere: RCSB PDB 4ANG · PDBe 4ANG · UniProt P03616
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