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Structure of thrombin bound to the inhibitor FM19
Analyse Structure of thrombin bound to the inhibitor FM19 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BV9
- Type
- protein
- Length
- 293 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; FM19 inhibitor
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- NA, IOD, NH2
- Pockets
- 3 · best druggability 0.34
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 29 | 31% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 259 | 14% helix, 34% strand | P00734 |
| C | FM19 inhibitor | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- IOD · Iodide ion · ion · 3 copies · chains B
- NH2 · Amino group · ion · chains C
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.34 | 0.76 | 16 | empty |
| 2 | 50 | 0.34 | 0.78 | 18 | IOD |
| 3 | 66 | 0.31 | 0.74 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1151 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 484 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 d-amino, 2 modified (disulfide, D-amino acid, nonstandard).
Compared structures
- 3BV9 · Structure of Thrombin Bound to the Inhibitor FM19 · 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 3BV9 · PDBe 3BV9 · UniProt P00734
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