Research workbench
RNA 15MER duplex binding with pzg monomer
Analyse RNA 15MER duplex binding with pzg monomer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KRG
- Type
- RNA
- Length
- 60 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3')
- Ligands
- PZG
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3') | rna | 15 | — | — |
Ligands and binding sites
- PZG · [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-(3-methyl-1~{H}-pyrazol-4-yl)phosphinic acid · ligand · 4 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.47 | 0.73 | 21 | empty |
| 2 | 238 | 0.43 | 0.72 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–D · 694 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- A–B · 693 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- A–C · 66 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 16 modified (nucleotide modification).
Compared structures
- 5KRG · RNA 15mer duplex binding with PZG monomer · 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
- Elsewhere: RCSB PDB 5KRG · PDBe 5KRG
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