Research workbench
HIV-1 dis kissing-loop in complex with ribostamycin
Analyse HIV-1 dis kissing-loop in complex with ribostamycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FCZ
- Type
- RNA
- Length
- 92 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 dis RNA
- Ligands
- RIO, K
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | HIV-1 dis RNA | rna | 23 | — | — |
Ligands and binding sites
- RIO · Ribostamycin · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.68 | 0.74 | 38 | RIO, K |
| 2 | 1065 | 0.67 | 0.74 | 44 | RIO, K |
Interfaces
5 interfaces between chains.
- C–D · 374 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- A–B · 369 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- B–D · 100 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- B–C · 95 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- A–D · 94 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 2FCZ · HIV-1 DIS kissing-loop in complex with ribostamycin · 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 2FCZ · PDBe 2FCZ
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