MolNFT v1 · #115542 · protein + DNA
X-ray structure of the complex between human alpha thrombin and a DUPLEX/QUADRUPLEX 31-mer DNA aptamer
5CMX · Alpha thrombin-light chain: “X-ray structure of the complex between human alpha thrombin and a DUPLEX/QUADRUPLEX 31-mer DNA aptamer”. X-ray diffraction, 2 ligands (0G6, K), 1 pocket (best druggability 0.57). MolNFT v1 #115542 on…
- PDB
- 5CMX
- Type
- protein + DNA
- Length
- 306 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha thrombin-light chain; Thrombin heavy chain; RE31
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6, K
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha thrombin-light chain (EC 3.4.21.5) | protein | 28 | 21% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 249 | 14% helix, 36% strand | P00734 |
| A | RE31 | dna | 29 | — | — |
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
- K · Potassium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.57 | 0.78 | 36 | 0G6 |
Interfaces
2 interfaces between chains.
- L–H · 1193 Ų buried · 20 hydrogen bonds · protein-protein
- H–A · 561 Ų buried · 17 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5CMX · X-ray structure of the complex between human alpha thrombin and a duplex/quadruplex… · the same entry in another collection · chain H against H, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain H against A, TM-score 0.92
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 5CMX · PDBe 5CMX · UniProt P00734
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