Research workbench
Thrombin in complex with inhibitor
Analyse Thrombin in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PKS
- Type
- protein
- Length
- 286 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain fragment; Hirudin
- UniProt
- P00734, P28504
- Ligands
- G44, NA
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain | protein | 27 | 33% helix, 0% strand | P00734 |
| B | Thrombin heavy chain fragment | protein | 147 | 11% helix, 37% strand | P00734 |
| C | Thrombin heavy chain fragment | protein | 102 | 17% helix, 32% strand | P00734 |
| D | Hirudin | protein | 10 | 30% helix, 0% strand | P28504 |
Ligands and binding sites
- G44 · 4-({[4-(3-methylbenzoyl)pyridin-2-yl]amino}methyl)benzenecarboximidamide · ligand · chains B, C
- NA · Sodium ion · metal · chains C
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 | 230 | 0.53 | 0.77 | 34 | G44 |
| 2 | 76 | 0.37 | 0.77 | 20 | empty |
| 3 | 58 | 0.31 | 0.76 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–C · 3320 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 838 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 637 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 582 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 42 Ų buried · 0 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 P28504
- Elsewhere: RCSB PDB 2PKS · PDBe 2PKS · UniProt P00734 · UniProt P28504
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