5DO4: Thrombin-RNA aptamer complex

PDB ID: 5DO4Download
MMDB ID: 143017
PDB Deposition Date: 2015/9/10
Updated in MMDB: 2023/10
Experimental Method:
x-ray diffraction
Resolution: 1.859  Å
Source Organism:
unidentified▼
Similar Structures:
Biological Unit for 5DO4: trimeric; determined by author and by software (PISA)
Molecular Components in 5DO4
Label Count Molecule
Proteins (2 molecules)
1
Thrombin Light Chain
Molecule annotation
1
Thrombin Heavy Chain
Molecule annotation
Nucleotide(1 molecule)
1
RNA (25-mer)
Molecule annotation
Chemicals and Non-standard biopolymers (11 molecules)
1
1
D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamideD-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
2
1
2-acetamido-2-deoxy-beta-D-glucopyranose2-acetamido-2-deoxy-beta-D-glucopyranose
3
4
1,2-ETHANEDIOL1,2-ETHANEDIOL
4
2
GLYCEROLGLYCEROL
5
1
CALCIUM IONCALCIUM ION
6
1
(4R)-2-METHYLPENTANE-2,4-DIOL(4R)-2-METHYLPENTANE-2,4-DIOL
7
1
MAGNESIUM IONMAGNESIUM ION
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303