Research workbench
X-ray structure of the complex of human alpha thrombin with the inhibitor sdz 229-357
Analyse X-ray structure of the complex of human alpha thrombin with the inhibitor sdz… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BHX
- Type
- protein
- Length
- 287 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha thrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- R56
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha thrombin (EC 3.4.21.5) | protein | 30 | 33% helix, 0% strand | P00734 |
| B | Alpha thrombin (EC 3.4.21.5) | protein | 147 | 11% helix, 37% strand | P00734 |
| F | Alpha thrombin (EC 3.4.21.5) | protein | 105 | 21% helix, 30% strand | P00734 |
| E | Alpha thrombin (EC 3.4.21.5) | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- R56 · 5-oxo-6-phenylmethanesulfonylamino-hexahydro-thiazolo[3,2-a]pyridine-3-carboxylic acid (3-guanidino-propyl)-amide · ligand · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.56 | 0.76 | 40 | R56 |
| 2 | 60 | 0.32 | 0.76 | 17 | empty |
| 3 | 51 | 0.28 | 0.75 | 12 | empty |
Interfaces
5 interfaces between chains.
- B–F · 3367 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 974 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 613 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 409 Ų buried · 4 hydrogen bonds · protein-protein
- F–E · 35 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1BHX · X-ray structure of the complex of human alpha thrombin with the inhibitor sdz 229-357 · the same entry in another collection · chain A against A, 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 1BHX · PDBe 1BHX · UniProt P00734
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