Research workbench
Crystal structure analysis of a novel oxyguanidine bound to thrombin
Analyse Crystal structure analysis of a novel oxyguanidine bound to thrombin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T4V
- Type
- protein
- Length
- 286 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; Hirudin iiia
- EC
- 3.4.21.5
- UniProt
- P00734, P28507
- Ligands
- 14A
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Prothrombin (EC 3.4.21.5) | protein | 26 | 38% helix, 0% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 249 | 14% helix, 36% strand | P00734 |
| I | Hirudin iiia | protein | 11 | 0% helix, 0% strand | P28507 |
Ligands and binding sites
- 14A · N-allyl-5-amidinoaminooxy-propyloxy-3-chloro-N-cyclopentylbenzamide · ligand · chains H
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 | 270 | 0.55 | 0.76 | 42 | 14A |
Interfaces
2 interfaces between chains.
- L–H · 1082 Ų buried · 25 hydrogen bonds · protein-protein
- H–I · 656 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
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
- Every structure of UniProt P28507
- Elsewhere: RCSB PDB 1T4V · PDBe 1T4V · UniProt P00734 · UniProt P28507
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