MolNFT v1 · #85037 · RNA
Catalytic RNA enzyme-product complex
488D · RNA ribozyme strand: “Catalytic RNA enzyme-product complex”. X-ray diffraction, 1 ligand (CD). MolNFT v1 #85037 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 488D
- Type
- RNA
- Length
- 66 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA ribozyme strand; First RNA fragment of cleaved substrate; Second RNA fragment of…
- Ligands
- CD
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA ribozyme strand | rna | 16 | — | — |
| B | First RNA fragment of cleaved substrate | rna | 20 | — | — |
| C | Second RNA fragment of cleaved substrate | rna | 5 | — | — |
| D | Uncleaved RNA substrate | rna | 25 | — | — |
Ligands and binding sites
- CD · Cadmium ion · metal · 8 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
4 interfaces between chains.
- A–D · 1021 Ų buried · 92 hydrogen bonds · nucleic-nucleic
- A–B · 760 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–C · 263 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- B–D · 224 Ų buried · 106 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 488D · Catalytic RNA enzyme-product complex · 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 488D · PDBe 488D
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