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Crystal structure of thrombin in complex with inhibitor
Analyse Crystal structure of 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
- 3DA9
- Type
- protein
- Length
- 287 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin peptide
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 44U, NA
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 27 | 37% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 251 | 16% helix, 35% strand | P00734 |
| D | Hirudin peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- 44U · beta-phenyl-D-phenylalanyl-N-propyl-L-prolinamide · ligand · chains B
- NA · Sodium ion · metal · chains B
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 | 264 | 0.55 | 0.77 | 41 | 44U |
| 2 | 52 | 0.29 | 0.76 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1087 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 608 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, phosphorylation).
Compared structures
- 3DA9 · Crystal structure of thrombin in complex with inhibitor · 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 3DA9 · PDBe 3DA9 · UniProt P00734
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