MolNFT v2 · #117070 · protein + RNA
Thrombin-RNA aptamer complex
5DO4: “Thrombin-RNA aptamer complex”. X-ray diffraction at 1.859, 3 ligands (NAG, CA, MG). MolNFT v2 #117070 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DO4
- Type
- protein + RNA
- Length
- 314 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.859
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- UniProt
- P00734
- Ligands
- NAG, CA, MG
Structure
x-ray diffraction · resolution 1.859 · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | — | protein | 32 | — | P00734 |
| H | — | protein | 257 | — | P00734 |
| A | — | rna | 25 | — | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- CA · Calcium ion · metal · chains H
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains H, L, A
- GOL · Glycerol · additive · 2 copies · chains L, H
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5DO4 · Thrombin-RNA aptamer 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
- Every structure of UniProt P00734
- Elsewhere: RCSB PDB 5DO4 · PDBe 5DO4 · UniProt P00734
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