Research workbench
Crystal structure of murine thrombin mutant W215A/E217A in complex with the extracellular fragment of human PAR1
Analyse Crystal structure of murine thrombin mutant W215A/E217A in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HKI
- Type
- protein
- Length
- 614 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Proteinase-activated receptor 1
- EC
- 3.4.21.5
- UniProt
- P19221, P25116
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · 6 distinct chains · 20% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 40 | 43% helix, 0% strand | P19221 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 255 | 15% helix, 34% strand | P19221 |
| C | Proteinase-activated receptor 1 | protein | 15 | 20% helix, 0% strand | P25116 |
| D | Thrombin light chain (EC 3.4.21.5) | protein | 43 | 49% helix, 0% strand | P19221 |
| E | Thrombin heavy chain (EC 3.4.21.5) | protein | 252 | 16% helix, 35% strand | P19221 |
| F | Proteinase-activated receptor 1 | protein | 9 | 0% helix, 0% strand | P25116 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.59 | 0.76 | 41 | empty |
| 2 | 298 | 0.57 | 0.77 | 43 | empty |
| 3 | 281 | 0.55 | 0.76 | 41 | empty |
| 4 | 130 | 0.47 | 0.78 | 30 | empty |
| 5 | 192 | 0.47 | 0.75 | 40 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1647 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1613 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 600 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 577 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 278 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3HKI · Crystal structure of murine thrombin mutant W215A/E217A in complex with the extracellular… · the same entry in another collection · chain B against B, TM-score 1.00
- P19221 · AlphaFold monomer V2.0 prediction for prothrombin (P19221) · a predicted model of the same protein · chain E against A, TM-score 0.98
- P25116 · AlphaFold monomer V2.0 prediction for proteinase-activated receptor 1 (P25116) · a predicted model of the same protein · chain F against A, TM-score 0.46
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 P25116
- Elsewhere: RCSB PDB 3HKI · PDBe 3HKI · UniProt P19221 · UniProt P25116
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