Research workbench
Complex of recombinant human thrombin with an inhibitor
Analyse Complex of recombinant human thrombin with an inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CF8
- Type
- protein
- Length
- 283 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin heavy chain; Hirudin iiia; Thrombin light chain
- EC
- 3.4.21.5
- UniProt
- P00734, P28508
- Ligands
- ESH, NA, CA
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 250 | 15% helix, 36% strand | P00734 |
| I | Hirudin iiia | protein | 5 | 0% helix, 0% strand | P28508 |
| L | Thrombin light chain (EC 3.4.21.5) | protein | 28 | 36% helix, 0% strand | P00734 |
Ligands and binding sites
- ESH · 4- [(1r,3as,4r,8as,8br)- 2- (4-chlorobenzyl)- 1-isopropyl- 3- oxodecahydropyrrolo[3,4- a]pyrrolizin-4- yl]benzenecarboximidamide · ligand · chains H
- NA · Sodium ion · metal · chains H
- CA · Calcium ion · metal · chains H
- SIN · Succinic acid · additive · chains H, I
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 | 269 | 0.56 | 0.77 | 40 | ESH |
Interfaces
2 interfaces between chains.
- H–L · 1133 Ų buried · 29 hydrogen bonds · protein-protein
- H–I · 402 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, additive adduct).
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 P28508
- Elsewhere: RCSB PDB 2CF8 · PDBe 2CF8 · UniProt P00734 · UniProt P28508
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