MolNFT v1 · #8775 · protein + DNA
Complex of human alpha-thrombin with a 15MER oligonucleotide ggttggtgtggttgg (based on X-ray model of DNA)
1HAP · 5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3': “Complex of human alpha-thrombin with a 15MER oligonucleotide ggttggtgtggttgg (based on X-ray model of DNA)”. X-ray diffraction, 1 ligand (0G6), 2 pockets (best druggability…
- PDB
- 1HAP
- Type
- protein + DNA
- Length
- 295 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'; Thrombin light chain; Thrombin…
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3' | dna | 15 | — | — |
| L | Thrombin light chain (EC 3.4.21.5) | protein | 27 | 19% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 253 | 10% helix, 34% strand | P00734 |
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
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 | 342 | 0.58 | 0.76 | 46 | 0G6 |
| 2 | 62 | 0.33 | 0.77 | 15 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1107 Ų buried · 23 hydrogen bonds · protein-protein
- D–H · 495 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 1HAP · Complex of human alpha-thrombin with a 15MER oligonucleotide ggttggtgtggttgg (based on… · 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 1HAP · PDBe 1HAP · UniProt P00734
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