Research workbench
X-ray structure of the complex between human alpha thrombin and NU172, a duplex/quadruplex 26-mer DNA aptamer, in the presence of sodium ions.
Analyse X-ray structure of the complex between human alpha thrombin and NU172, a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GN7
- Type
- protein + DNA
- Length
- 317 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Prothrombin; NU172, DNA (26-mer)
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6, NAG, BMA, MAN, GAL, SIA, NA
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · resolution 2.8 · 3 distinct chains · 15% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Prothrombin (EC 3.4.21.5) | protein | 33 | 30% helix, 0% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 258 | 13% helix, 33% strand | P00734 |
| E | NU172, DNA (26-mer) | dna | 26 | — | — |
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 · 3 copies · chains H
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- GAL · beta-D-galactopyranose · sugar
- SIA · N-acetyl-alpha-neuraminic acid · sugar
- NA · Sodium ion · metal · 2 copies · chains H, E
- GOL · Glycerol · additive · chains H, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.59 | 0.77 | 50 | 0G6 |
| 2 | 58 | 0.36 | 0.78 | 15 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1391 Ų buried · 33 hydrogen bonds · protein-protein
- H–E · 608 Ų buried · 17 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide, 2 covalent, 1 glycan (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 6GN7 · PDBe 6GN7 · UniProt P00734
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