MolNFT v1 · #119003 · RNA
Structure of the standard kink turn hmkt-7 as stem loop in P212121 space group
5FJ1: “Structure of the standard kink turn hmkt-7 as stem loop in P212121 space group”. X-ray diffraction, 2 ligands (MG, NA), 6 pockets (best druggability 0.57). MolNFT v1 #119003 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5FJ1
- Type
- RNA
- Length
- 192 nucleotides
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hmkt-7
- Ligands
- MG, NA
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Hmkt-7 | rna | 24 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 21 copies · chains A, B, C, D, E, F, G
- NA · Sodium ion · metal · 3 copies · chains A, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.57 | 0.72 | 35 | empty |
| 2 | 541 | 0.55 | 0.72 | 34 | MG |
| 3 | 123 | 0.41 | 0.77 | 10 | empty |
| 4 | 130 | 0.41 | 0.76 | 11 | empty |
| 5 | 132 | 0.41 | 0.76 | 10 | empty |
Interfaces
8 interfaces between chains.
- A–E · 375 Ų buried · 19 hydrogen bonds · nucleic-nucleic
- B–C · 374 Ų buried · 18 hydrogen bonds · nucleic-nucleic
- D–F · 374 Ų buried · 18 hydrogen bonds · nucleic-nucleic
- G–H · 372 Ų buried · 18 hydrogen bonds · nucleic-nucleic
- D–G · 245 Ų buried · 8 hydrogen bonds · nucleic-nucleic
Compared structures
- 5FJ1 · Structure of the standard kink turn HmKt-7 as stem loop in P212121 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 5FJ1 · PDBe 5FJ1
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