MolNFT v1 · #119002 · RNA
Structure of the standard kink turn hmkt-7 as simple duplex in P4222 space group
5FJ0: “Structure of the standard kink turn hmkt-7 as simple duplex in P4222 space group”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.65). MolNFT v1 #119002 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FJ0
- Type
- RNA
- Length
- 57 nucleotides
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hmkt-7
- Ligands
- MG
- Pockets
- 1 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hmkt-7 | rna | 19 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.65 | 0.76 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1320 Ų buried · 118 hydrogen bonds · nucleic-nucleic
- B–C · 123 Ų buried · 5 hydrogen bonds · nucleic-nucleic
- A–C · 43 Ų buried · 1 hydrogen bond · nucleic-nucleic
Compared structures
- 5FJ0 · Structure of the standard kink turn HmKt-7 as simple duplex in P4222 space group · 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 5FJ0 · PDBe 5FJ0
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