MolNFT v1 · #84983 · RNA
5'-R(*UP*AP*GP*CP*CP*CP*C)-3', 5'-R(*GP*GP*GP*GP*CP*UP*A)-3'
435D · RNA (5'-R(*UP*AP*GP*CP*CP*CP*C)-3'): “5'-R(*UP*AP*GP*CP*CP*CP*C)-3', 5'-R(*GP*GP*GP*GP*CP*UP*A)-3'”. X-ray diffraction, 1 ligand (NA). MolNFT v1 #84983 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 435D
- Type
- RNA
- Length
- 28 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*UP*AP*GP*CP*CP*CP*C)-3'); RNA (5'-R(*GP*GP*GP*GP*CP*UP*A)-3')
- Ligands
- NA
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA (5'-R(*UP*AP*GP*CP*CP*CP*C)-3') | rna | 7 | — | — |
| B, D | RNA (5'-R(*GP*GP*GP*GP*CP*UP*A)-3') | rna | 7 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
5 interfaces between chains.
- A–B · 341 Ų buried · 29 hydrogen bonds · nucleic-nucleic
- C–D · 341 Ų buried · 27 hydrogen bonds · nucleic-nucleic
- B–D · 104 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- A–C · 89 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- B–C · 66 Ų buried · 1 hydrogen bond · nucleic-nucleic
Compared structures
- 435D · 5'-R(*UP*AP*GP*CP*CP*CP*C)-3', 5'-R(*GP*GP*GP*GP*CP*UP*A)-3' · 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 435D · PDBe 435D
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