Research workbench
Human alpha-thrombin complexed with ac-(D)PHE-pro-boro-N- butyl-amidino-glycine-oh
Analyse Human alpha-thrombin complexed with ac-(D)PHE-pro-boro-N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LHE
- Type
- protein
- Length
- 282 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin; Hirudin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- DI3
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (EC 3.4.21.5) | protein | 26 | 31% helix, 0% strand | P00734 |
| H | Alpha-thrombin (EC 3.4.21.5) | protein | 249 | 14% helix, 35% strand | P00734 |
| I | Hirudin | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- DI3 · Ac-(d)phe-pro-boro-N-butyl-amidino-glycine-oh · 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 | 251 | 0.56 | 0.77 | 39 | DI3 |
| 2 | 58 | 0.34 | 0.78 | 16 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1116 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 470 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 1LHE · Human alpha-thrombin complexed with ac-(D)PHE-pro-boro-N-butyl-amidino-glycine-oh · the same entry in another collection · chain L against L, TM-score 1.00
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 1LHE · PDBe 1LHE · UniProt P00734
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