Research workbench
Thrombin-RNA aptamer complex
Analyse Thrombin-RNA aptamer complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DO4
- Type
- protein + RNA
- Length
- 313 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.859
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Thrombin light chain; Thrombin heavy chain; RNA (25-mer)
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6, NAG, CA, MG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.859 · 3 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 32 | 31% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 256 | 16% helix, 35% strand | P00734 |
| A | RNA (25-mer) | rna | 25 | — | — |
Ligands and binding sites
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- CA · Calcium ion · metal · chains H
- MG · Magnesium ion · metal · chains H, A
- EDO · 1,2-ethanediol · additive · 4 copies · chains L, H, 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.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.77 | 0.96 | 24 | EDO, MRD |
| 2 | 251 | 0.56 | 0.78 | 41 | 0G6 |
| 3 | 89 | 0.46 | 0.81 | 16 | MG |
| 4 | 126 | 0.42 | 0.76 | 13 | empty |
| 5 | 93 | 0.38 | 0.76 | 17 | GOL |
Interfaces
3 interfaces between chains.
- L–H · 1241 Ų buried · 31 hydrogen bonds · protein-protein
- H–A · 1009 Ų buried · 20 hydrogen bonds · protein-nucleic
- L–A · 99 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 11 modified, 4 disulfide, 2 covalent, 1 glycan (nucleotide modification, disulfide, covalent ligand, N-glycosylation).
Compared structures
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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