Research workbench
Crystal structure of the human thrombin mutant D102N in complex with the extracellular fragment of human PAR4.
Analyse Crystal structure of the human thrombin mutant D102N 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
- 3QDZ
- Type
- protein
- Length
- 579 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 4
- EC
- 3.4.21.5
- UniProt
- P00734, Q96RI0
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Thrombin light chain (EC 3.4.21.5) | protein | 29 | 17% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 251 | 13% helix, 32% strand | P00734 |
| D | Thrombin heavy chain (EC 3.4.21.5) | protein | 257 | 11% helix, 30% strand | P00734 |
| E | Proteinase-activated receptor 4 | protein | 9 | 0% helix, 33% strand | Q96RI0 |
| F | Proteinase-activated receptor 4 | protein | 4 | 0% helix, 25% strand | Q96RI0 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 832 | 0.73 | 0.78 | 68 | empty |
| 2 | 59 | 0.61 | 0.91 | 22 | empty |
| 3 | 53 | 0.54 | 0.89 | 17 | empty |
| 4 | 79 | 0.32 | 0.74 | 16 | empty |
| 5 | 63 | 0.32 | 0.76 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1190 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1184 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 540 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 461 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 445 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3QDZ · Crystal structure of the human thrombin mutant D102N in complex with the extracellular… · the same entry in another collection · chain F against F, TM-score 1.00
- Q96RI0 · AlphaFold monomer V2.0 prediction for proteinase-activated receptor 4 (Q96RI0) · a predicted model of the same protein · chain F against A, TM-score 0.95
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 Q96RI0
- Elsewhere: RCSB PDB 3QDZ · PDBe 3QDZ · UniProt P00734 · UniProt Q96RI0
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