Research workbench
Crystal structure of murine thrombin in complex with the extracellular fragment of murine PAR4
Analyse Crystal structure of murine thrombin in complex with the extracellular fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PV9
- Type
- protein
- Length
- 327 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Proteinase-activated receptor 4
- UniProt
- P19221, O88634
- Ligands
- NAG
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain | protein | 43 | 19% helix, 0% strand | P19221 |
| B | Thrombin heavy chain | protein | 258 | 13% helix, 34% strand | P19221 |
| C | Proteinase-activated receptor 4 | protein | 26 | 0% helix, 8% strand | O88634 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.44 | 0.76 | 22 | empty |
| 2 | 71 | 0.36 | 0.77 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1721 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1105 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2PV9 · Crystal structure of murine thrombin in complex with the extracellular fragment of murine… · the same entry in another collection · chain A against A, TM-score 1.00
- P19221 · AlphaFold monomer V2.0 prediction for prothrombin (P19221) · a predicted model of the same protein · chain B against A, TM-score 0.97
- O88634 · AlphaFold monomer V2.0 prediction for proteinase-activated receptor 4 (O88634) · a predicted model of the same protein · chain C against A, TM-score 0.27
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 P19221
- Every structure of UniProt O88634
- Elsewhere: RCSB PDB 2PV9 · PDBe 2PV9 · UniProt P19221 · UniProt O88634
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